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Munaò G, Saija F, Cassone G. The structure of water-ammonia mixtures from classical and ab initio molecular dynamics. J Chem Phys 2024; 161:094503. [PMID: 39230374 DOI: 10.1063/5.0220328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Accepted: 08/21/2024] [Indexed: 09/05/2024] Open
Abstract
The structure of aqueous ammonia solutions is investigated through classical molecular dynamics (MD) and ab initio molecular dynamics (AIMD) simulations. We have preliminarily compared three well-known classical force fields for liquid water (SPC, SPC/E, and TIP4P) in order to identify the most accurate one in reproducing AIMD results obtained at the Generalized Gradient Approximation (GGA) and meta-GGA levels of theory. Liquid ammonia has been simulated by implementing an optimized force field recently developed by Chettiyankandy et al. [Fluid Phase Equilib. 511, 112507 (2020)]. Analysis of the radial distribution functions for different ammonia concentrations reveals that the three water force fields provide comparable estimates of the mixture structure, with the SPC/E performing slightly better. Although a fairly good agreement between MD and AIMD is observed for conditions close to the equimolarity, at lower ammonia concentrations, important discrepancies arise, with classical force fields underestimating the number and strength of H-bonds between water molecules and between water and ammonia moieties. Here, we prove that these drawbacks are rooted in a poor sampling of the configurational space spanned by the hydrogen atoms lying in the H-bonds of H2O⋯H2O and, more critically, H2O⋯NH3 neighbors due to the lack of polarization and charge transfer terms. This way, non-polarizable classical force fields underestimate the proton affinity of the nitrogen atom of ammonia in aqueous solutions, which plays a key role under realistic dilute ammonia conditions. Our results witness the need for developing more suited polarizable models that are able to take into account these effects properly.
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Affiliation(s)
- Gianmarco Munaò
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, 98166 Messina, Italy
| | - Franz Saija
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
| | - Giuseppe Cassone
- Institute for Chemical-Physical Processes, National Research Council of Italy (IPCF-CNR), 98158 Messina, Italy
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2
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Patkar D, Bharati Ahirwar M, Deshmukh MM. A Tug of War between the Self- and Cross-associating Hydrogen Bonds in Neutral Ammonia-Water Clusters: Energetic Insights by Molecular Tailoring Approach. Chemphyschem 2022; 23:e202200476. [PMID: 36127809 DOI: 10.1002/cphc.202200476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 09/09/2022] [Indexed: 01/05/2023]
Abstract
In the present work, the energies of various types of individual HBs observed in neutral (NH3 )m (H2 O)n , (m+n=2 to 7) clusters were estimated using the molecular tailoring approach (MTA)-based method. The calculated individual HB energies suggest that the O-H…N HBs are the strongest (1.21 to 12.49 kcal mol-1 ). The next ones are the O-H…O (3.97 to 9.30 kcal mol-1 ) HBs. The strengths of N-H…N (1.09 to 5.29 kcal mol-1 ) and N-H…O (2.85 to 5.56 kcal mol-1 ) HBs are the weakest. The HB energies in dimers also follow this rank ordering. However, the HB energies in dimers are much smaller than those obtained by the MTA-based method due to the loss in cooperativity contribution in the dimers. Thus, the calculated cooperativity contributions, for different types of HBs, fall in the range 0.64 to 5.73 kcal mol-1 . We wish to emphasize based on the energetic rank ordering obtained by the MTA-based method that the O-H of water is a better HB donor than the N-H of ammonia. The reasons for the observed energetic rank ordering are two folds: (i) intrinsically stronger O-H…N HBs than the O-H…O ones as revealed by dimer energies and (ii) the higher cooperativity contribution in the former than the later ones. Indeed, the MTA-based method is useful in providing the missing energetic rank ordering of various type of HBs in neutral (NH3 )m (H2 O)n clusters, in the literature.
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Affiliation(s)
- Deepak Patkar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), 470003, Sagar, India
| | - Mini Bharati Ahirwar
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), 470003, Sagar, India
| | - Milind M Deshmukh
- Department of Chemistry, Dr. Harisingh Gour Vishwavidyalaya, (A Central University), 470003, Sagar, India
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3
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Harold SE, Bready CJ, Juechter LA, Kurfman LA, Vanovac S, Fowler VR, Mazaleski GE, Odbadrakh TT, Shields GC. Hydrogen-Bond Topology Is More Important Than Acid/Base Strength in Atmospheric Prenucleation Clusters. J Phys Chem A 2022; 126:1718-1728. [PMID: 35235333 DOI: 10.1021/acs.jpca.1c10754] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We explored the hypothesis that on the nanoscale level, acids and bases might exhibit different behavior than in bulk solution. Our study system consisted of sulfuric acid, formic acid, ammonia, and water. We calculated highly accurate Domain-based Local pair-Natural Orbital- Coupled-Cluster/Complete Basis Set (DLPNO-CCSD(T)/CBS) energies on DFT geometries and used the resulting Gibbs free energies for cluster formation to compute the overall equilibrium constants for every possible cluster. The equilibrium constants combined with the initial monomer concentrations were used to predict the formation of clusters at the top and the bottom of the troposphere. Our results show that formic acid is as effective as ammonia at forming clusters with sulfuric acid and water. The structure of formic acid is uniquely suited to form hydrogen bonds with sulfuric acid. Additionally, it can partner with water to form bridges from one side of sulfuric acid to the other, hence demonstrating that hydrogen bonding topology is more important than acid/base strength in these atmospheric prenucleation clusters.
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Affiliation(s)
- Shannon E Harold
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Conor J Bready
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Leah A Juechter
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Luke A Kurfman
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sara Vanovac
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Vance R Fowler
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Grace E Mazaleski
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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4
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Tóth Z, Kubečka J, Muchová E, Slavíček P. Ionization energies in solution with the QM:QM approach. Phys Chem Chem Phys 2020; 22:10550-10560. [PMID: 32010902 DOI: 10.1039/c9cp06154a] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We discuss a fragment-based QM:QM scheme as a practical way to access the energetics of vertical electronic processes in the condensed phase. In the QM:QM scheme, we decompose the large molecular system into small fragments, which interact solely electrostatically. The energies of the fragments are calculated in a self-consistent field generated by the other fragments and the total energy of the system is calculated as a sum of the fragment energies. We show on two test cases (cytosine and a sodium cation) that the method allows one to accurately simulate the shift of vertical ionization energies (VIE) while going from the gas phase to the bulk. For both examples, the predicted solvent shifts and peak widths estimated at the DFT level agree well with the experimental observations. We argue that the QM:QM approach is more suitable than either an electrostatic embedding based QM/MM approach, a full quantum description at the DFT level with a generally used functional or a combination of both. We also discuss the potential scope of the applicability for other electronic processes such as Auger decay.
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Affiliation(s)
- Zsuzsanna Tóth
- University of Chemistry and Technology Prague, Department of Physical Chemistry, Technická 5, 16628 Prague 6, Czech Republic.
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5
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Kulkarni AD. Molecular Hydration of Carbonic Acid: Ab Initio Quantum Chemical and Density Functional Theory Investigation. J Phys Chem A 2019; 123:5504-5516. [PMID: 31244117 DOI: 10.1021/acs.jpca.9b01122] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular hydration of carbonic acid (H2CO3) is investigated in terms of bonding patterns in H2CO3···(H2O) n [ n = 1-4] hydrogen-bonded clusters within ab initio quantum chemical and density functional theory (DFT) frameworks. Successive addition of water molecules to H2CO3···H2O entails elongation of O-H (hydroxyl) bond as well as contraction of specific intermolecular hydrogen bonds signifying hydration of carbonic acid; these structural features get markedly enhanced under the continuum solvation framework. A comparison between the structurally similar clusters H2CO3···(H2O) n and HCOOH···(H2O) n [ n = 1-3] brings out the structural stability of the former. The present investigation in conjunction with the binding energy behavior of approaching water molecule(s) should serve as a precursor for pathways exploring aqueous dissociation of H2CO3 for larger clusters, as well as development of force-field potentials for acid dissociation process.
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Affiliation(s)
- Anant D Kulkarni
- Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore 560012 , India
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6
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Zhang L, Li W, Fang T, Li S. Accurate Relative Energies and Binding Energies of Large Ice–Liquid Water Clusters and Periodic Structures. J Phys Chem A 2017; 121:4030-4038. [DOI: 10.1021/acs.jpca.7b03376] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lei Zhang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wei Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Tao Fang
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Shuhua Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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7
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Anacker T, Tew DP, Friedrich J. First UHF Implementation of the Incremental Scheme for Open-Shell Systems. J Chem Theory Comput 2015; 12:65-78. [PMID: 26605975 DOI: 10.1021/acs.jctc.5b00933] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The incremental scheme makes it possible to compute CCSD(T) correlation energies to high accuracy for large systems. We present the first extension of this fully automated black-box approach to open-shell systems using an Unrestricted Hartree-Fock (UHF) wave function, extending the efficient domain-specific basis set approach to handle open-shell references. We test our approach on a set of organic and metal organic structures and molecular clusters and demonstrate standard deviations from canonical CCSD(T) values of only 1.35 kJ/mol using a triple ζ basis set. We find that the incremental scheme is significantly more cost-effective than the canonical implementation even for relatively small systems and that the ease of parallelization makes it possible to perform high-level calculations on large systems in a few hours on inexpensive computers. We show that the approximations that make our approach widely applicable are significantly smaller than both the basis set incompleteness error and the intrinsic error of the CCSD(T) method, and we further demonstrate that incremental energies can be reliably used in extrapolation schemes to obtain near complete basis set limit CCSD(T) reaction energies for large systems.
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Affiliation(s)
- Tony Anacker
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
| | - David P Tew
- School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom
| | - Joachim Friedrich
- Institute for Chemistry, Chemnitz University of Technology , Straße der Nationen 62, D-09111 Chemnitz, Sachsen, Germany
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8
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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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9
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Wang B, Yang KR, Xu X, Isegawa M, Leverentz HR, Truhlar DG. Quantum mechanical fragment methods based on partitioning atoms or partitioning coordinates. Acc Chem Res 2014; 47:2731-8. [PMID: 24841937 DOI: 10.1021/ar500068a] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Conspectus The development of more efficient and more accurate ways to represent reactive potential energy surfaces is a requirement for extending the simulation of large systems to more complex systems, longer-time dynamical processes, and more complete statistical mechanical sampling. One way to treat large systems is by direct dynamics fragment methods. Another way is by fitting system-specific analytic potential energy functions with methods adapted to large systems. Here we consider both approaches. First we consider three fragment methods that allow a given monomer to appear in more than one fragment. The first two approaches are the electrostatically embedded many-body (EE-MB) expansion and the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE), which we have shown to yield quite accurate results even when one restricts the calculations to include only electrostatically embedded dimers. The third fragment method is the electrostatically embedded molecular tailoring approach (EE-MTA), which is more flexible than EE-MB and EE-MB-CE. We show that electrostatic embedding greatly improves the accuracy of these approaches compared with the original unembedded approaches. Quantum mechanical fragment methods share with combined quantum mechanical/molecular mechanical (QM/MM) methods the need to treat a quantum mechanical fragment in the presence of the rest of the system, which is especially challenging for those parts of the rest of the system that are close to the boundary of the quantum mechanical fragment. This is a delicate matter even for fragments that are not covalently bonded to the rest of the system, but it becomes even more difficult when the boundary of the quantum mechanical fragment cuts a bond. We have developed a suite of methods for more realistically treating interactions across such boundaries. These methods include redistributing and balancing the external partial atomic charges and the use of tuned fluorine atoms for capping dangling bonds, and we have shown that they can greatly improve the accuracy. Finally we present a new approach that goes beyond QM/MM by combining the convenience of molecular mechanics with the accuracy of fitting a potential function to electronic structure calculations on a specific system. To make the latter practical for systems with a large number of degrees of freedom, we developed a method to interpolate between local internal-coordinate fits to the potential energy. A key issue for the application to large systems is that rather than assigning the atoms or monomers to fragments, we assign the internal coordinates to reaction, secondary, and tertiary sets. Thus, we make a partition in coordinate space rather than atom space. Fits to the local dependence of the potential energy on tertiary coordinates are arrayed along a preselected reaction coordinate at a sequence of geometries called anchor points; the potential energy function is called an anchor points reactive potential. Electrostatically embedded fragment methods and the anchor points reactive potential, because they are based on treating an entire system by quantum mechanical electronic structure methods but are affordable for large and complex systems, have the potential to open new areas for accurate simulations where combined QM/MM methods are inadequate.
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Affiliation(s)
- Bo Wang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Ke R. Yang
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Miho Isegawa
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Hannah R. Leverentz
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
| | - Donald G. Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant St. SE, Minneapolis, Minnesota 55455-0431, United States
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10
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Barnes TA, Goodpaster JD, Manby FR, Miller TF. Accurate basis set truncation for wavefunction embedding. J Chem Phys 2014; 139:024103. [PMID: 23862925 DOI: 10.1063/1.4811112] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Density functional theory (DFT) provides a formally exact framework for performing embedded subsystem electronic structure calculations, including DFT-in-DFT and wavefunction theory-in-DFT descriptions. In the interest of efficiency, it is desirable to truncate the atomic orbital basis set in which the subsystem calculation is performed, thus avoiding high-order scaling with respect to the size of the MO virtual space. In this study, we extend a recently introduced projection-based embedding method [F. R. Manby, M. Stella, J. D. Goodpaster, and T. F. Miller III, J. Chem. Theory Comput. 8, 2564 (2012)] to allow for the systematic and accurate truncation of the embedded subsystem basis set. The approach is applied to both covalently and non-covalently bound test cases, including water clusters and polypeptide chains, and it is demonstrated that errors associated with basis set truncation are controllable to well within chemical accuracy. Furthermore, we show that this approach allows for switching between accurate projection-based embedding and DFT embedding with approximate kinetic energy (KE) functionals; in this sense, the approach provides a means of systematically improving upon the use of approximate KE functionals in DFT embedding.
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Affiliation(s)
- Taylor A Barnes
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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11
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Saha A, Raghavachari K. Dimers of Dimers (DOD): A New Fragment-Based Method Applied to Large Water Clusters. J Chem Theory Comput 2013; 10:58-67. [DOI: 10.1021/ct400472v] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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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12
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Jia X, Wang X, Liu J, Zhang JZH, Mei Y, He X. An improved fragment-based quantum mechanical method for calculation of electrostatic solvation energy of proteins. J Chem Phys 2013; 139:214104. [DOI: 10.1063/1.4833678] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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13
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Ramabhadran RO, Raghavachari K. Extrapolation to the Gold-Standard in Quantum Chemistry: Computationally Efficient and Accurate CCSD(T) Energies for Large Molecules Using an Automated Thermochemical Hierarchy. J Chem Theory Comput 2013; 9:3986-94. [PMID: 26592394 DOI: 10.1021/ct400465q] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The CCSD(T) method is known as the gold-standard in quantum chemistry and has been the method of choice in quantum chemistry for over 20 years to obtain accurate bond energies and molecular properties. Its computational cost formally scales as the seventh power of the size of the system and can be prohibitive for large molecules. As part of our efforts to reduce the computational cost of the CCSD(T) method yet retain its accuracy, we present a simple, efficient, and user-friendly protocol to extrapolate to CCSD(T) energies in conjunction with MP2 energies. The method is based on the automated error-canceling thermochemical hierarchy previously developed by us called the Connectivity-Based Hierarchy (CBH). For a test set containing 30 diverse nonaromatic organic molecules and biomonomers, we obtain highly accurate extrapolated CCSD(T) energies (with a mean absolute error of only 0.2-0.3 kcal/mol with different basis-set). Additionally, the work also features the successful extrapolation to CCSD energies using a similar protocol.
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Affiliation(s)
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University , Bloomington, Indiana 47405, United States
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14
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Kurbanov EK, Leverentz HR, Truhlar DG, Amin EA. Analysis of the Errors in the Electrostatically Embedded Many-Body Expansion of the Energy and the Correlation Energy for Zn and Cd Coordination Complexes with Five and Six Ligands and Use of the Analysis to Develop a Generally Successful Fragmentation Strategy. J Chem Theory Comput 2013; 9:2617-2628. [PMID: 23814509 DOI: 10.1021/ct4001872] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present paper, we apply the electrostatically embedded many-body expansion of the correlation energy (EE-MB-CE) to the calculation of zinc-ligand and cadmium-ligand bond dissociation energies, and we analyze the errors due to various fragmentation schemes in a variety of neutral, positively charged, and negatively charged Zn2+ and Cd2+ coordination complexes. As a result of the analysis, we are able to present a new, simple, and unambiguous fragmentation strategy. Following this strategy, we show that both methods perform well for zinc-ligand and cadmium-ligand bond dissociation energies for all systems studied in the paper, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor (LF), which has garnered substantial attention as a target for drug development. To draw general conclusions we consider ten pentacoordinate and hexacoordinate zinc and cadmium containing coordination complexes, each with 10 or 15 different fragmentation schemes. By analyzing errors, we developed a prescription for the optimal fragmentation strategy. With this scheme, and using MP2 correlation energies as a test, we find that the electrostatically embedded three-body expansion of the correlation energy (EE-3B-CE) method is able to reproduce all 53 conventionally calculated bond energies with an average absolute error of only 0.59 kcal/mol. The paper also presents EE-MB-CE calculations using the CCSD(T) level of theory on an LF model system. With CCSD(T), EE-3B-CE has an average error of 0.30 kcal/mol.
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Affiliation(s)
- Elbek K Kurbanov
- Department of Medicinal Chemistry, Department of Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, MN 55414
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15
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Orabi EA, Lamoureux G. Polarizable Interaction Model for Liquid, Supercritical, and Aqueous Ammonia. J Chem Theory Comput 2013; 9:2035-51. [DOI: 10.1021/ct301123j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esam A. Orabi
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
| | - Guillaume Lamoureux
- Department of Chemistry
and Biochemistry and Centre
for Research in Molecular Modeling (CERMM), Concordia University,
7141 Sherbrooke Street West, Montréal, Québec H4B 1R6,
Canada
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16
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Li W. Linear scaling explicitly correlated MP2-F12 and ONIOM methods for the long-range interactions of the nanoscale clusters in methanol aqueous solutions. J Chem Phys 2013; 138:014106. [DOI: 10.1063/1.4773011] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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17
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Mayhall NJ, Raghavachari K. Many-Overlapping-Body (MOB) Expansion: A Generalized Many Body Expansion for Nondisjoint Monomers in Molecular Fragmentation Calculations of Covalent Molecules. J Chem Theory Comput 2012; 8:2669-75. [DOI: 10.1021/ct300366e] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas J. Mayhall
- 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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18
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Le HA, Tan HJ, Ouyang JF, Bettens RPA. Combined Fragmentation Method: A Simple Method for Fragmentation of Large Molecules. J Chem Theory Comput 2012; 8:469-78. [DOI: 10.1021/ct200783n] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hai-Anh Le
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Hwee-Jia Tan
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - 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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19
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Vianello R, Mavri J. Microsolvation of the histamine monocation in aqueous solution: the effect on structure, hydrogen bonding ability and vibrational spectrum. NEW J CHEM 2012. [DOI: 10.1039/c2nj20877f] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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20
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Fletcher GD, Fedorov DG, Pruitt SR, Windus TL, Gordon MS. Large-Scale MP2 Calculations on the Blue Gene Architecture Using the Fragment Molecular Orbital Method. J Chem Theory Comput 2011; 8:75-9. [DOI: 10.1021/ct200548v] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Graham D. Fletcher
- Argonne Leadership Computing Facility, Argonne, Illinois 60439, United States
| | - Dmitri G. Fedorov
- National Institute of Advanced Industrial Science and Technology, Tsukuba, Japan
| | - Spencer R. Pruitt
- Iowa State University and Ames Laboratory, Ames, Iowa 50011, United States
| | - Theresa L. Windus
- Iowa State University and Ames Laboratory, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Iowa State University and Ames Laboratory, Ames, Iowa 50011, United States
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21
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Fedorov DG, Kitaura K. Energy Decomposition Analysis in Solution Based on the Fragment Molecular Orbital Method. J Phys Chem A 2011; 116:704-19. [DOI: 10.1021/jp209579w] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dmitri G. Fedorov
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
| | - Kazuo Kitaura
- NRI, National Institute of Advanced Industrial Science and Technology (AIST), Central 2, Umezono 1-1-1, Tsukuba, 305-8568, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan
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22
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Kurbanov EK, Leverentz HR, Truhlar DG, Amin EA. Electrostatically Embedded Many-Body Expansion for Neutral and Charged Metalloenzyme Model Systems. J Chem Theory Comput 2011; 8:1-5. [PMID: 22639556 DOI: 10.1021/ct200637v] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The electrostatically embedded many-body (EE-MB) method has proven accurate for calculating cohesive and conformational energies in clusters, and it has recently been extended to obtain bond dissociation energies for metal-ligand bonds in positively charged inorganic coordination complexes. In the present paper, we present four key guidelines that maximize the accuracy and efficiency of EE-MB calculations for metal centers. Then, following these guidelines, we show that the EE-MB method can also perform well for bond dissociation energies in a variety of neutral and negatively charged inorganic coordination systems representing metalloenzyme active sites, including a model of the catalytic site of the zinc-bearing anthrax toxin lethal factor, a popular target for drug development. In particular, we find that the electrostatically embedded three-body (EE-3B) method is able to reproduce conventionally calculated bond-breaking energies in a series of pentacoordinate and hexacoordinate zinc-containing systems with an average absolute error (averaged over 25 cases) of only 0.98 kcal/mol.
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Affiliation(s)
- Elbek K Kurbanov
- Department of Medicinal Chemistry, Department of Chemistry, and Minnesota Supercomputing Institute, University of Minnesota, Minneapolis, MN 55414
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23
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Gordon MS, Fedorov DG, Pruitt SR, Slipchenko LV. Fragmentation Methods: A Route to Accurate Calculations on Large Systems. Chem Rev 2011; 112:632-72. [DOI: 10.1021/cr200093j] [Citation(s) in RCA: 836] [Impact Index Per Article: 64.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Mark S. Gordon
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Dmitri G. Fedorov
- Nanosystem Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), 1-1-1 Umezono, Tsukuba, Ibaraki 305-8568, Japan
| | - Spencer R. Pruitt
- Department of Chemistry and Ames Laboratory, Iowa State University, Ames Iowa 50011, United States
| | - Lyudmila V. Slipchenko
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
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24
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Mayhall NJ, Raghavachari K. Molecules-in-Molecules: An Extrapolated Fragment-Based Approach for Accurate Calculations on Large Molecules and Materials. J Chem Theory Comput 2011; 7:1336-43. [DOI: 10.1021/ct200033b] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas J. Mayhall
- 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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25
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Hua D, Leverentz HR, Amin EA, Truhlar DG. Assessment and Validation of the Electrostatically Embedded Many-Body Expansion for Metal−Ligand Bonding. J Chem Theory Comput 2010; 7:251-5. [DOI: 10.1021/ct100491q] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Duy Hua
- Department of Chemistry, Department of Medicinal Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Hannah R. Leverentz
- Department of Chemistry, Department of Medicinal Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Elizabeth A. Amin
- Department of Chemistry, Department of Medicinal Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Donald G. Truhlar
- Department of Chemistry, Department of Medicinal Chemistry, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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26
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QM/MM Approaches to the Electronic Spectra of Hydrogen-Bonding Systems with Connection to Many-Body Decomposition Schemes. ADVANCES IN QUANTUM CHEMISTRY 2010. [DOI: 10.1016/s0065-3276(10)59004-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
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27
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Mata RA, Stoll H, Cabral BJC. A Simple One-Body Approach to the Calculation of the First Electronic Absorption Band of Water. J Chem Theory Comput 2009; 5:1829-37. [DOI: 10.1021/ct9001653] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ricardo A. Mata
- Grupo de Física-Matemática da Universidade de Lisboa, Avenue Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - Hermann Stoll
- Grupo de Física-Matemática da Universidade de Lisboa, Avenue Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
| | - B. J. Costa Cabral
- Grupo de Física-Matemática da Universidade de Lisboa, Avenue Professor Gama Pinto 2, 1649-003 Lisboa, Portugal, Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany, and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, 1749-016, Lisboa, Portugal
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28
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Leverentz HR, Truhlar DG. Electrostatically Embedded Many-Body Approximation for Systems of Water, Ammonia, and Sulfuric Acid and the Dependence of Its Performance on Embedding Charges. J Chem Theory Comput 2009; 5:1573-84. [DOI: 10.1021/ct900095d] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Hannah R. Leverentz
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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29
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Suárez E, Díaz N, Suárez D. Thermochemical Fragment Energy Method for Biomolecules: Application to a Collagen Model Peptide. J Chem Theory Comput 2009; 5:1667-79. [DOI: 10.1021/ct8005002] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ernesto Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
| | - Natalia Díaz
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
| | - Dimas Suárez
- Departamento de Química Física y Analítica, Universidad de Oviedo, 33006 Oviedo (Asturias), Spain
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30
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Siuda P, Uras-Aytemiz N, Sadlej J. Microsolvation of HCl within Cold NH3 Clusters. J Phys Chem A 2008; 112:11423-30. [DOI: 10.1021/jp802687u] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Paweł Siuda
- Department of Chemistry, Suleyman Demirel University, 32260 Isparta, Turkey, and Department of Chemistry, University of Warsaw, Pasteur 1, 02-093 Warsaw, Poland
| | - Nevin Uras-Aytemiz
- Department of Chemistry, Suleyman Demirel University, 32260 Isparta, Turkey, and Department of Chemistry, University of Warsaw, Pasteur 1, 02-093 Warsaw, Poland
| | - Joanna Sadlej
- Department of Chemistry, Suleyman Demirel University, 32260 Isparta, Turkey, and Department of Chemistry, University of Warsaw, Pasteur 1, 02-093 Warsaw, Poland
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