1
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Hasan MN, Ray M, Saha A. Landscape of In Silico Tools for Modeling Covalent Modification of Proteins: A Review on Computational Covalent Drug Discovery. J Phys Chem B 2023; 127:9663-9684. [PMID: 37921534 DOI: 10.1021/acs.jpcb.3c04710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2023]
Abstract
Covalent drug discovery has been a challenging research area given the struggle of finding a sweet balance between selectivity and reactivity for these drugs, the lack of which often leads to off-target activities and hence undesirable side effects. However, there has been a resurgence in covalent drug design following the success of several covalent drugs such as boceprevir (2011), ibrutinib (2013), neratinib (2017), dacomitinib (2018), zanubrutinib (2019), and many others. Design of covalent drugs includes many crucial factors, where "evaluation of the binding affinity" and "a detailed mechanistic understanding on covalent inhibition" are at the top of the list. Well-defined experimental techniques are available to elucidate these factors; however, often they are expensive and/or time-consuming and hence not suitable for high throughput screens. Recent developments in in silico methods provide promise in this direction. In this report, we review a set of recent publications that focused on developing and/or implementing novel in silico techniques in "Computational Covalent Drug Discovery (CCDD)". We also discuss the advantages and disadvantages of these approaches along with what improvements are required to make it a great tool in medicinal chemistry in the near future.
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Affiliation(s)
- Md Nazmul Hasan
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
| | - Manisha Ray
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois 60660, United States
| | - Arjun Saha
- Department of Chemistry and Biochemistry, University of Wisconsin─Milwaukee, Milwaukee, Wisconsin 53211, United States
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2
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Olive LN, Dornshuld EV, Schaefer HF, Tschumper GS. Competition between Solvent···Solvent and Solvent···Solute Interactions in the Microhydration of the Tetrafluoroborate Anion, BF 4-(H 2O) n=1,2,3,4. J Phys Chem A 2023; 127:8806-8820. [PMID: 37774368 DOI: 10.1021/acs.jpca.3c04014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
This study systematically examines the interactions of the tetrafluoroborate anion (BF4-) with up to four water molecules (BF4-(H2O)n=1,2,3,4). Full geometry optimizations and subsequent harmonic vibrational frequency computations are performed using a variety of density functional theory (DFT) methods (B3LYP, B3LYP-D3BJ, and M06-2X) and the MP2 ab initio method with a triple-ζ correlation consistent basis set augmented with diffuse functions on all non-hydrogen atoms (cc-pVTZ for H and aug-cc-pVTZ for B, O, and F; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the CCSD(T) ab initio method and the haTZ basis set for the mono- and dihydrate (n = 1, 2) structures. The 2-body:Many-body (2b:Mb) technique, in which CCSD(T) computations capture the 1- and 2-body contributions to the interactions and MP2 computations recover all higher-order contributions, was used to extend these demanding computations to the tri- and tetrahydrate (n = 3, 4) systems. Four, five, and eight new stationary points have been identified for the di-, tri-, and tetrahydrate systems, respectively. The global minimum of the monohydrate adopts a symmetric double ionic hydrogen bond motif with C2v symmetry and an electronic dissociation energy of 13.17 kcal mol-1 at the CCSD(T)/haTZ level of theory. This strong solvent···solute interaction, however, competes with solute···solute interactions in the lowest-energy BF4-(H2O)n=2,3,4 minima that are not seen in the other di-, tri-, or tetrahydrate minima. The latter interactions help increase the 2b:Mb dissociation energies to more than 26, 41, and 51 kcal mol-1 for n = 2, 3, and 4, respectively. Structures that form hydrogen bonds between the solvating water molecules also exhibit the largest shifts in the harmonic OH stretching frequencies for the waters of hydration. These shifts can exceed -280 cm-1 relative to an isolated H2O molecule at the 2b:Mb/haTZ level of theory.
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Affiliation(s)
- Laura N Olive
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Eric V Dornshuld
- Department of Chemistry, Mississippi State University, Mississippi State, Mississippi 39762, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Gregory S Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, Mississippi 38677, United States
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3
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Werner HJ, Hansen A. Accurate Calculation of Isomerization and Conformational Energies of Larger Molecules Using Explicitly Correlated Local Coupled Cluster Methods in Molpro and ORCA. J Chem Theory Comput 2023; 19:7007-7030. [PMID: 37486154 DOI: 10.1021/acs.jctc.3c00270] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
An overview of the approximations in the explicitly correlated local coupled cluster methods PNO-LCCSD(T)-F12 in Molpro and DLPNO-CCSD(T)F12 in ORCA is given. Options to select the domains of projected atomic orbitals (PAOs), pair natural orbitals (PNOs), and triples natural orbitals (TNOs) in both programs are described and compared in detail. The two programs are applied to compute isomerization and conformational energies of the ISOL24 and ACONFL test sets, where the former is part of the GMTKN55 benchmark suite. Thorough studies of basis set effects are presented for selected systems. These revealed large intramolecular basis set superposition effects that make it practically impossible to reliably determine the complete basis set (CBS) limits without including explicitly correlated terms. The latter strongly reduce the basis set dependence and at the same time also errors caused by the local domain approximations. On the basis of these studies, the PNO-LCCSD(T)-F12 method is applied to determine new reference energies for the above-mentioned benchmark sets. We are confident that our results should agree within a few tenths of a kcal mol-1 with the (unknown) CCSD(T)/CBS values, which therefore allowed us to define computational settings for accurate explicitly correlated local coupled cluster methods with moderate computational effort. With these protocols, especially PNO-LCCSD(T)-F12b/AVTZ', reliable reference values for comprehensive benchmark sets can be generated efficiently. This can significantly advance the development and evaluation of the performance of approximate electronic structure methods, especially improved density functional approximations or machine learning approaches.
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Affiliation(s)
- Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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4
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Wang Z, Liu W. iOI: An Iterative Orbital Interaction Approach for Solving the Self-Consistent Field Problem. J Chem Theory Comput 2021; 17:4831-4845. [PMID: 34240856 DOI: 10.1021/acs.jctc.1c00445] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An iterative orbital interaction (iOI) approach is proposed to solve, in a bottom-up fashion, the self-consistent field problem in quantum chemistry. While it belongs grossly to the family of fragment-based quantum chemical methods, iOI is distinctive in that (1) it divides and conquers not only the energy but also the wave function and that (2) the subsystem sizes are automatically determined by successively merging neighboring small subsystems until they are just enough for converging the wave function to a given accuracy. Orthonormal occupied and virtual localized molecular orbitals are obtained in a natural manner, which can be used for all post-SCF purposes.
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Affiliation(s)
- Zikuan Wang
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, P. R. China
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5
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Tripathy V, Saha A, Raghavachari K. Electrostatically embedded molecules-in-molecules approach and its application to molecular clusters. J Comput Chem 2021; 42:719-734. [PMID: 33586802 DOI: 10.1002/jcc.26492] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 11/25/2020] [Accepted: 01/16/2021] [Indexed: 11/06/2022]
Abstract
We report the application of our fragment-based quantum chemistry model MIM (Molecules-In-Molecules) with electrostatic embedding. The method is termed "EE-MIM (Electrostatically Embedded Molecules-In-Molecules)" and accounts for the missing electrostatic interactions in the subsystems resulting from fragmentation. Point charges placed at the atomic positions are used to represent the interaction of each subsystem with the rest of the molecule with minimal increase in the computational cost. We have carefully calibrated this model on a range of different sizes of clusters containing up to 57 water molecules. The fragmentation methods have been applied with the goal of reproducing the unfragmented total energy at the MP2/6-311G(d,p) level. Comparative analysis has been carried out between MIM and EE-MIM to gauge the impact of electrostatic embedding. Performance of several different parameters such as the type of charge and levels of fragmentation are analyzed for the prediction of absolute energies. The use of background charges in subsystem calculations improves the performance of both one- and two-layer MIM while it is noticeably important in the case of one-layer MIM. Embedded charges for two-layer MIM are obtained from a full system calculation at the low-level. For one-layer MIM, in the absence of a full system calculation, two different types of embedded charges, namely, Geometry dependent (GD) and geometry independent (GI) charges, are used. A self-consistent procedure is employed to obtain GD charges. We have further tested our method on challenging charged systems with stronger intermolecular interactions, namely, protonated ammonia clusters (containing up to 30 ammonia molecules). The observations are similar to water clusters with improved performance using embedded charges. Overall, the performance of NPA charges as embedded charges is found to be the best.
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Affiliation(s)
- Vikrant Tripathy
- Department of Chemistry, Indiana University, Bloomington, Indiana, USA
| | - Arjun Saha
- Department of Chemistry, University of Southern California, Los Angeles, California, USA
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 8. Explicitly Correlated Open-Shell Coupled-Cluster with Pair Natural Orbitals PNO-RCCSD(T)-F12 and PNO-UCCSD(T)-F12. J Chem Theory Comput 2021; 17:902-926. [PMID: 33405921 DOI: 10.1021/acs.jctc.0c01129] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We present explicitly correlated open-shell pair natural orbital local coupled-cluster methods, PNO-RCCSD(T)-F12 and PNO-UCCSD(T)-F12. The methods are extensions of our previously reported PNO-R/UCCSD methods (J. Chem. Theory Comput., 2020, 16, 3135-3151, https://pubs.acs.org/doi/10.1021/acs.jctc.0c00192) with additions of explicit correlation and perturbative triples corrections. The explicit correlation treatment follows the spin-orbital CCSD-F12b theory using Ansatz 3*A, which is found to yield comparable or better basis set convergence than the more rigorous Ansatz 3C in computed ionization potentials and reaction energies using double- to quaduple-ζ basis sets. The perturbative triples correction is adapted from the spin-orbital (T) theory to use triples natural orbitals (TNOs). To address the coupling due to off-diagonal Fock matrix elements, the local triples amplitudes are iteratively solved using small domains of TNOs, and a semicanonical (T0) domain correction with larger domains is applied to reduce the domain errors. The performance of the methods is demonstrated through benchmark calculations on ionization potentials, radical stabilization energies, reaction energies of fragmentations and rearrangements in radical cations, and spin-state energy differences of iron complexes. For a few test sets where canonical calculations are feasible, PNO-RCCSD(T)-F12 results agree with the canonical ones to within 0.4 kcal mol-1, and this maximum error is reduced to below 0.2 kcal mol-1 when large local domains are used. For larger systems, results using different thresholds for the local approximations are compared to demonstrate that 1 kcal mol-1 level of accuracy can be achieved using our default settings. For a couple of difficult cases, it is demonstrated that the errors from individual approximations are only a fraction of 1 kcal mol-1, and the overall accuracy of the method does not rely on error compensations. In contrast to canonical calculations, the use of spin-orbitals does not lead to a significant increase of computational time and memory usage in the most expensive steps of PNO-R/UCCSD(T)-F12 calculations. The only exception is the iterative solution of the (T) amplitudes, which can be avoided without significant errors by using a perturbative treatment of the off-diagonal coupling, known as (T1) approximation. For most systems, even the semicanonical approximation (T0) leads only to small errors in relative energies. Our program is well parallelized and capable of computing accurate correlation energies for molecules with 100-200 atoms using augmented triple-ζ basis sets in less than a day of elapsed time on a small computer cluster.
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Affiliation(s)
- Qianli Ma
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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7
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Sadhukhan T, Beckett D, Thapa B, Raghavachari K. Coupling Constants, High Spin, and Broken Symmetry States of Organic Radicals: an Assessment of the Molecules-in-Molecules Fragmentation-Based Method. J Chem Theory Comput 2019; 15:5998-6009. [DOI: 10.1021/acs.jctc.9b00563] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Tumpa Sadhukhan
- Department of Chemistry, Indiana University, Bloomington, 47405 Indiana, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington, 47405 Indiana, United States
| | - Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington, 47405 Indiana, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, 47405 Indiana, United States
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8
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Krause C, Werner HJ. Scalable Electron Correlation Methods. 6. Local Spin-Restricted Open-Shell Second-Order Møller-Plesset Perturbation Theory Using Pair Natural Orbitals: PNO-RMP2. J Chem Theory Comput 2019; 15:987-1005. [PMID: 30571916 DOI: 10.1021/acs.jctc.8b01012] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present a (near) linear scaling implementation of high-spin open-shell Møller-Plesset perturbation theory using pair natural orbitals (PNO-RMP2). The theory is based on a new variant of open-shell MP2 which is fully spin-adapted and uses a single set of spin-free amplitudes, as in closed-shell MP2. This method, denoted SROMP2, is invariant to unitary orbital transformations within the closed, open, and virtual orbital subspaces. Accordingly, only a single set of PNOs per spatial orbital pair is needed, and the efficiency is similar to closed-shell calculations. The PNOs are obtained using a semicanonical approximation with large domains of projected atomic orbitals (PAOs). Linear scaling is achieved provided that the open-shell orbitals are local, and distant pairs are treated by multipole approximations. The method is efficiently parallelized. The convergence of ionization and reaction energies as a function of the PAO and PNO domain sizes is demonstrated and found to be very similar as for closed-shell calculations. The suitability of the PNOs for explicitly correlated PNO-RCCSD-F12 calculations is also tested. So far, this method is only simulated using a conventional program with appropriate projections to the PAO and PNO subspaces. It is demonstrated for radical stabilization energies as well as ionization potentials that the errors caused by the local domain approximations with our default thresholds are negligible.
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Affiliation(s)
- Christine Krause
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie , Universität Stuttgart , Pfaffenwaldring 55 , D-70569 Stuttgart , Germany
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9
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Ma Q, Werner H. Explicitly correlated local coupled‐cluster methods using pair natural orbitals. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2018. [DOI: 10.1002/wcms.1371] [Citation(s) in RCA: 100] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Qianli Ma
- Institute for Theoretical ChemistryUniversity of StuttgartStuttgartGermany
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10
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Thapa B, Beckett D, Jovan Jose KV, Raghavachari K. Assessment of Fragmentation Strategies for Large Proteins Using the Multilayer Molecules-in-Molecules Approach. J Chem Theory Comput 2018; 14:1383-1394. [DOI: 10.1021/acs.jctc.7b01198] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Bishnu Thapa
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Daniel Beckett
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - K. V. Jovan Jose
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington 47405, Indiana, United States
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11
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Li HJ, Yan D, Cai HQ, Yi HB, Min XB, Xia FF. Insights into water-mediated ion clustering in aqueous CaSO 4 solutions: pre-nucleation cluster characteristics studied by ab initio calculations and molecular dynamics simulations. Phys Chem Chem Phys 2018; 19:11390-11403. [PMID: 28422226 DOI: 10.1039/c7cp00428a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The molecular structure of growth units building crystals is a fundamental issue in the crystallization processes from aqueous solutions. In this work, a systematic investigation of pre-nucleation clusters and their hydration characteristics in aqueous CaSO4 solutions was performed using ab initio calculations and molecular dynamics (MD) simulations. The results of ab initio calculations and MD simulations indicate that the dominant species in aqueous CaSO4 solutions are monodentate ion-associated structures. Compared with charged ion clusters, neutral clusters are more likely to be present in an aqueous CaSO4 solution. Neutral (CaSO4)m clusters are probably the growth units involved in the pre-nucleation or crystallization processes. Meanwhile, hydration behavior around ion associated species in aqueous CaSO4 solutions plays an important role in related phase/polymorphism selections. Upon ion clustering, the residence of some water molecules around Ca2+ in ion-associated species is weakened while that of some bridging waters is enhanced due to dual interaction by Ca2+ and SO42-. Some phase/polymorphism selections can be achieved in aqueous CaSO4 solutions by controlling the hydration around pre-nucleation clusters. Moreover, the association trend between calcium and sulfate is found to be relatively strong, which hints at the low solubility of calcium sulfate in water.
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Affiliation(s)
- Hui-Ji Li
- State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha 410082, China.
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12
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Ghosh S, Andersen A, Gagliardi L, Cramer CJ, Govind N. Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians. J Chem Theory Comput 2017; 13:4410-4420. [DOI: 10.1021/acs.jctc.7b00618] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumen Ghosh
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Amity Andersen
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
| | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Cramer
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Niranjan Govind
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
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13
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Schwilk M, Ma Q, Köppl C, Werner HJ. Scalable Electron Correlation Methods. 3. Efficient and Accurate Parallel Local Coupled Cluster with Pair Natural Orbitals (PNO-LCCSD). J Chem Theory Comput 2017; 13:3650-3675. [DOI: 10.1021/acs.jctc.7b00554] [Citation(s) in RCA: 100] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Max Schwilk
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Qianli Ma
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Christoph Köppl
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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14
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Yao K, Herr JE, Parkhill J. The many-body expansion combined with neural networks. J Chem Phys 2017; 146:014106. [PMID: 28063436 DOI: 10.1063/1.4973380] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Fragmentation methods such as the many-body expansion (MBE) are a common strategy to model large systems by partitioning energies into a hierarchy of decreasingly significant contributions. The number of calculations required for chemical accuracy is still prohibitively expensive for the ab initio MBE to compete with force field approximations for applications beyond single-point energies. Alongside the MBE, empirical models of ab initio potential energy surfaces have improved, especially non-linear models based on neural networks (NNs) which can reproduce ab initio potential energy surfaces rapidly and accurately. Although they are fast, NNs suffer from their own curse of dimensionality; they must be trained on a representative sample of chemical space. In this paper we examine the synergy of the MBE and NN's and explore their complementarity. The MBE offers a systematic way to treat systems of arbitrary size while reducing the scaling problem of large systems. NN's reduce, by a factor in excess of 106, the computational overhead of the MBE and reproduce the accuracy of ab initio calculations without specialized force fields. We show that for a small molecule extended system like methanol, accuracy can be achieved with drastically different chemical embeddings. To assess this we test a new chemical embedding which can be inverted to predict molecules with desired properties. We also provide our open-source code for the neural network many-body expansion, Tensormol.
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Affiliation(s)
- Kun Yao
- Department of Chemistry, University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - John E Herr
- Department of Chemistry, University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
| | - John Parkhill
- Department of Chemistry, University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, USA
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15
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Chen GD, Weng J, Song G, Li ZH. Generalized Switch Functions in the Multilevel Many-Body Expansion Method and Its Application to Water Clusters. J Chem Theory Comput 2017; 13:2010-2020. [DOI: 10.1021/acs.jctc.7b00144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Guo Dong Chen
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jingwei Weng
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Guoliang Song
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Zhen Hua Li
- Collaborative Innovation Center of Chemistry for Energy Material, Shanghai Key Laboratory of Molecular Catalysis & Innovative Materials, Department of Chemistry, Fudan University, Shanghai 200433, China
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16
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Gao Z, Ding Y, Yang W, Han W. DFT study of water adsorption on lignite molecule surface. J Mol Model 2017; 23:27. [PMID: 28064378 DOI: 10.1007/s00894-016-3194-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2016] [Accepted: 12/15/2016] [Indexed: 11/30/2022]
Abstract
High moisture content is a main characteristic of low-rank coal, such as lignite. Numerous oxygen containing functional groups in lignite make it represent some special properties, and these functional groups affect the adsorption mechanisms of water molecules on lignite surface. This study reports some typical water · · · lignite conformations, along with a detailed analysis of the geometry, electrostatic potential distribution, reduced density gradient of interaction, and interaction energy decomposition. The results show that water molecules tend to aggregate around functional groups, and hydrogen bonds play a dominant role in the interaction. The adsorption energy of water cluster on lignite surface is larger than that of isolated water molecule, a good linear relationship between the interaction distance and adsorption energy of layers has been found. Since water is a polar molecule, the local minima and maxima of electrostatic potential in conformations increase along with more water adsorbing on lignite surface. Reduced density gradient analysis shows that H-bonds, van der Waals interaction, and a little steric make up the interaction between water cluster and lignite molecule. In these studied conformations which mainly are H-bond complexes, electrostatic and exchange repulsion play a dominant role, whereas polarization and dispersion make relatively small contribution to the interaction. Attractive and repulsive interaction both affect the stability of water · · · lignite conformations.
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Affiliation(s)
- Zhengyang Gao
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
| | - Yi Ding
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
| | - Weijie Yang
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China.
| | - Wentao Han
- The Department of Power Engineering, North China Electric Power University, Baoding, 071003, China
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17
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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18
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Saha A, Raghavachari K. Analysis of Different Fragmentation Strategies on a Variety of Large Peptides: Implementation of a Low Level of Theory in Fragment-Based Methods Can Be a Crucial Factor. J Chem Theory Comput 2016; 11:2012-23. [PMID: 26574406 DOI: 10.1021/ct501045s] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We have investigated the performance of two classes of fragmentation methods developed in our group (Molecules-in-Molecules (MIM) and Many-Overlapping-Body (MOB) expansion), to reproduce the unfragmented MP2 energies on a test set composed of 10 small to large biomolecules. They have also been assessed to recover the relative energies of different motifs of the acetyl(ala)18NH2 system. Performance of different bond-cutting environments and the use of Hartree-Fock and different density functionals (as a low level of theory) in conjunction with the fragmentation strategies have been analyzed. Our investigation shows that while a low level of theory (for recovering long-range interactions) may not be necessary for small peptides, it provides a very effective strategy to accurately reproduce the total and relative energies of larger peptides such as the different motifs of the acetyl(ala)18NH2 system. Employing M06-2X as the low level of theory, the calculated mean total energy deviation (maximum deviation) in the total MP2 energies for the 10 molecules in the test set at MIM(d=3.5Å), MIM(η=9), and MOB(d=5Å) are 1.16 (2.31), 0.72 (1.87), and 0.43 (2.02) kcal/mol, respectively. The excellent performance suggests that such fragment-based methods should be of general use for the computation of accurate energies of large biomolecular systems.
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Affiliation(s)
- Arjun Saha
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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19
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Zhang J, Dolg M. Third-Order Incremental Dual-Basis Set Zero-Buffer Approach for Large High-Spin Open-Shell Systems. J Chem Theory Comput 2016; 11:962-8. [PMID: 26579750 DOI: 10.1021/ct501052e] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The third-order incremental dual-basis set zero-buffer approach (inc3-db-B0) is an efficient, accurate, and black-box quantum chemical method for obtaining correlation energies of large systems, and it has been successfully applied to many real chemical problems. In this work, we extend this approach to high-spin open-shell systems. In the open-shell approach, we will first decompose the occupied orbitals of a system into several domains by a K-means clustering algorithm. The essential part is that we preserve the active (singly occupied) orbitals in all the calculations of the domain correlation energies. The duplicated contributions of the active orbitals to the correlation energy are subtracted from the incremental expansion. All techniques of truncating the virtual space such as the B0 approximation can be applied. This open-shell inc3-db-B0 approach is combined with the CCSD and CCSD(T) methods and applied to the computations of a singlet-triplet gap and an electron detachment process. Our approach exhibits an accuracy better than 0.6 kcal/mol or 0.3 eV compared with the standard implementation, while it saves a large amount of the computational time and can be efficiently parallelized.
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Affiliation(s)
- Jun Zhang
- Institute for Theoretical Chemistry, University of Cologne , Greinstraße 4, D-50939 Cologne, Germany
| | - Michael Dolg
- Institute for Theoretical Chemistry, University of Cologne , Greinstraße 4, D-50939 Cologne, Germany
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20
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Yuan D, Shen X, Li W, Li S. Are fragment-based quantum chemistry methods applicable to medium-sized water clusters? Phys Chem Chem Phys 2016; 18:16491-500. [DOI: 10.1039/c6cp01931e] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
The GEBF method is demonstrated to be more accurate than the EE-MB method for medium-sized water clusters.
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Affiliation(s)
- Dandan Yuan
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Xiaoling Shen
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Wei Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
| | - Shuhua Li
- School of Chemistry and Chemical Engineering
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education
- Institute of Theoretical and Computational Chemistry
- Nanjing University
- Nanjing
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21
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Ma Q, Werner HJ. Scalable Electron Correlation Methods. 2. Parallel PNO-LMP2-F12 with Near Linear Scaling in the Molecular Size. J Chem Theory Comput 2015; 11:5291-304. [DOI: 10.1021/acs.jctc.5b00843] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qianli Ma
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Baden-Württemberg, Germany
| | - Hans-Joachim Werner
- Institut für Theoretische
Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Baden-Württemberg, Germany
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22
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Sahu N, Gadre SR, Rakshit A, Bandyopadhyay P, Miliordos E, Xantheas SS. Low energy isomers of (H2O)25 from a hierarchical method based on Monte Carlo temperature basin paving and molecular tailoring approaches benchmarked by MP2 calculations. J Chem Phys 2015; 141:164304. [PMID: 25362296 DOI: 10.1063/1.4897535] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We report new global minimum candidate structures for the (H2O)25 cluster that are lower in energy than the ones reported previously and correspond to hydrogen bonded networks with 42 hydrogen bonds and an interior, fully coordinated water molecule. These were obtained as a result of a hierarchical approach based on initial Monte Carlo Temperature Basin Paving sampling of the cluster's Potential Energy Surface with the Effective Fragment Potential, subsequent geometry optimization using the Molecular Tailoring Approach with the fragments treated at the second order Møller-Plesset (MP2) perturbation (MTA-MP2) and final refinement of the entire cluster at the MP2 level of theory. The MTA-MP2 optimized cluster geometries, constructed from the fragments, were found to be within <0.5 kcal/mol from the minimum geometries obtained from the MP2 optimization of the entire (H2O)25 cluster. In addition, the grafting of the MTA-MP2 energies yields electronic energies that are within <0.3 kcal/mol from the MP2 energies of the entire cluster while preserving their energy rank order. Finally, the MTA-MP2 approach was found to reproduce the MP2 harmonic vibrational frequencies, constructed from the fragments, quite accurately when compared to the MP2 ones of the entire cluster in both the HOH bending and the OH stretching regions of the spectra.
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Affiliation(s)
- Nityananda Sahu
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Shridhar R Gadre
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016, India
| | - Avijit Rakshit
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Pradipta Bandyopadhyay
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi 110067, India
| | - Evangelos Miliordos
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
| | - Sotiris S Xantheas
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, Richland, Washington 99352, USA
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23
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Affiliation(s)
- John F. Ouyang
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
| | - Ryan P. A. Bettens
- Department of Chemistry, National University of Singapore, 3 Science
Drive 3, Singapore 117543
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24
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Sengupta A, Ramabhadran RO, Raghavachari K. Breaking a bottleneck: Accurate extrapolation to “gold standard” CCSD(T) energies for large open shell organic radicals at reduced computational cost. J Comput Chem 2015; 37:286-95. [DOI: 10.1002/jcc.24050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Revised: 07/14/2015] [Accepted: 07/20/2015] [Indexed: 11/11/2022]
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25
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Sahu N, Khire SS, Gadre SR. Structures, energetics and vibrational spectra of (H2O)32clusters: a journey from model potentials to correlated theory. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1062150] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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26
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 760] [Impact Index Per Article: 84.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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27
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Akimov AV, Prezhdo OV. Large-Scale Computations in Chemistry: A Bird’s Eye View of a Vibrant Field. Chem Rev 2015; 115:5797-890. [DOI: 10.1021/cr500524c] [Citation(s) in RCA: 159] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Alexey V. Akimov
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
| | - Oleg V. Prezhdo
- Department
of Chemistry, University of South California, Los Angeles, California 90089, United States
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28
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Raghavachari K, Saha A. Accurate Composite and Fragment-Based Quantum Chemical Models for Large Molecules. Chem Rev 2015; 115:5643-77. [PMID: 25849163 DOI: 10.1021/cr500606e] [Citation(s) in RCA: 183] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Krishnan Raghavachari
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Arjun Saha
- Department of Chemistry, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
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29
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Affiliation(s)
- Michael A Collins
- †Research School of Chemistry, Australian National University, Canberra, ACT 0200, Australia
| | - Ryan P A Bettens
- ‡Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
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30
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Alipour M. Relative energies of water nanoclusters (H2O)20: comparison of empirical and nonempirical double-hybrids with generalized energy-based fragmentation approach. NEW J CHEM 2015. [DOI: 10.1039/c5nj00817d] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The applicability of recently developed parameterized and parameter-free double-hybrids for predicting the relative energies of water nanoclusters has been examined.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz
- Iran
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31
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Ramabhadran RO, Raghavachari K. The successful merger of theoretical thermochemistry with fragment-based methods in quantum chemistry. Acc Chem Res 2014; 47:3596-604. [PMID: 25393551 DOI: 10.1021/ar500294s] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
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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Affiliation(s)
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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32
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Gao J, Truhlar DG, Wang Y, Mazack MJM, Löffler P, Provorse MR, Rehak P. Explicit polarization: a quantum mechanical framework for developing next generation force fields. Acc Chem Res 2014; 47:2837-45. [PMID: 25098651 PMCID: PMC4165456 DOI: 10.1021/ar5002186] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
Molecular mechanical force fields have been successfully used to
model condensed-phase and biological systems for a half century. By
means of careful parametrization, such classical force fields can
be used to provide useful interpretations of experimental findings
and predictions of certain properties. Yet, there is a need to further
improve computational accuracy for the quantitative prediction of
biomolecular interactions and to model properties that depend on the
wave functions and not just the energy terms. A new strategy called
explicit polarization (X-Pol) has been developed to construct the
potential energy surface and wave functions for macromolecular and
liquid-phase simulations on the basis of quantum mechanics rather
than only using quantum mechanical results to fit analytic force fields.
In this spirit, this approach is called a quantum mechanical force
field (QMFF). X-Pol is a general fragment method for electronic
structure calculations
based on the partition of a condensed-phase or macromolecular system
into subsystems (“fragments”) to achieve computational
efficiency. Here, intrafragment energy and the mutual electronic polarization
of interfragment interactions are treated explicitly using quantum
mechanics. X-Pol can be used as a general, multilevel electronic structure
model for macromolecular systems, and it can also serve as a new-generation
force field. As a quantum chemical model, a variational many-body
(VMB) expansion approach is used to systematically improve interfragment
interactions, including exchange repulsion, charge delocalization,
dispersion, and other correlation energies. As a quantum mechanical
force field, these energy terms are approximated by empirical functions
in the spirit of conventional molecular mechanics. This Account first
reviews the formulation of X-Pol, in the full variationally correct
version, in the faster embedded version, and with systematic many-body
improvements. We discuss illustrative examples involving water clusters
(which show the power of two-body corrections), ethylmethylimidazolium
acetate ionic liquids (which reveal that the amount of charge transfer
between anion and cation is much smaller than what has been assumed
in some classical simulations), and a solvated protein in aqueous
solution (which shows that the average charge distribution of carbonyl
groups along the polypeptide chain depends strongly on their position
in the sequence, whereas they are fixed in most classical force fields).
The development of QMFFs also offers an opportunity to extend the
accuracy of biochemical simulations to areas where classical force
fields are often insufficient, especially in the areas of spectroscopy,
reactivity, and enzyme catalysis.
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Affiliation(s)
- Jiali Gao
- Theoretical
Chemistry Institute, State Key Laboratory of Theoretical and Computational
Chemistry, Jilin University, Changchun, Jilin Province 130028, People’s Republic of China
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Donald G. Truhlar
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Yingjie Wang
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Michael J. M. Mazack
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Patrick Löffler
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Makenzie R. Provorse
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Pavel Rehak
- Department
of Chemistry and Supercomputing Institute University of Minnesota, Minneapolis, Minnesota 55455, United States
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