1
|
Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
Collapse
Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| |
Collapse
|
2
|
Nochebuena J, Liu S, Cisneros GA. Relative cooperativity in neutral and charged molecular clusters using QM/MM calculations. J Chem Phys 2024; 160:134301. [PMID: 38557841 DOI: 10.1063/5.0203020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 03/13/2024] [Indexed: 04/04/2024] Open
Abstract
QM/MM methods have been used to study electronic structure properties and chemical reactivity in complex molecular systems where direct electronic structure calculations are not feasible. In our previous work, we showed that non-polarizable force fields, by design, describe intermolecular interactions through pairwise interactions, overlooking many-body interactions involving three or more particles. In contrast, polarizable force fields account partially for many-body effects through polarization, but still handle van der Waals and permanent electrostatic interactions pairwise. We showed that despite those limitations, polarizable and non-polarizable force fields can reproduce relative cooperativity achieved using density functional theory due to error compensation mechanisms. In this contribution, we assess the performance of QM/MM methods in reproducing these phenomena. Our study highlights the significance of the QM region size and force field choice in QM/MM calculations, emphasizing the importance of parameter validation to obtain accurate interaction energy predictions.
Collapse
Affiliation(s)
- Jorge Nochebuena
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, North Carolina 27599, USA
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - G Andrés Cisneros
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, USA
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, USA
| |
Collapse
|
3
|
Hix MA, Walker AR. AutoParams: An Automated Web-Based Tool To Generate Force Field Parameters for Molecular Dynamics Simulations. J Chem Inf Model 2023; 63:6293-6301. [PMID: 37773638 DOI: 10.1021/acs.jcim.3c01049] [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
Many research questions benefit from molecular dynamics simulations to observe the motions and conformations of molecules over time, which rely on force fields that describe sets of common molecules by category. With the increase of importance for large data sets used in machine learning and growing computational efficiency, the ability to rapidly create large numbers of force field inputs is of high importance. Unusual molecules, such as nucleotide analogues, functionalized carbohydrates, and modified amino acids, are difficult to describe consistently using standard force fields, requiring the development of custom parameters for each unique molecule. While these parameters may be created by individual users, the process can become time-consuming or may introduce errors that may not be immediately apparent. We present an open-source automated parameter generation service, AutoParams, which requires minimal input from the user and creates useful Amber force field parameter sets for most molecules, particularly those that combine molecular types (e.g., a carbohydrate functionalized with a benzene). We include hierarchical atom-typing logic that makes it straightforward to expand with additional force fields and settings, and options for creating monomers in polymers, such as functionalized amino acids. It can be straightforwardly linked to any charge generation program and currently has interfaces to Psi4, PsiRESP, and TeraChem. It is open source and is available via GitHub. It includes error checking and testing protocols to ensure the parameters will be sufficient for subsequent molecular dynamics simulations and streamlines the creation of force field databases.
Collapse
Affiliation(s)
- Mark A Hix
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| | - Alice R Walker
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202-3489, United States
| |
Collapse
|
4
|
Csizi K, Reiher M. Universal
QM
/
MM
approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
| | - Markus Reiher
- Laboratorium für Physikalische Chemie ETH Zürich Zürich Switzerland
| |
Collapse
|
5
|
Taylor M, Yu H, Ho J. Predicting Solvent Effects on S N2 Reaction Rates: Comparison of QM/MM, Implicit, and MM Explicit Solvent Models. J Phys Chem B 2022; 126:9047-9058. [PMID: 36300819 DOI: 10.1021/acs.jpcb.2c06000] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Solvents are one of the key variables in the optimization of a synthesis yield or properties of a synthesis product. In this paper, contemporary solvent models are applied to predict the rates of SN2 reactions in a range of aqueous and non-aqueous solvents. High-level CCSD(T)/CBS//M06-2X/6-31+G(d) gas phase energies were combined with solvation free energies from SMD, SM12, and ADF-COSMO-RS continuum solvent models, as well as molecular mechanics (MM) explicit solvent models with different atomic charge schemes to predict the rate constants of three SN2 reactions in eight protic and aprotic solvents. It is revealed that the prediction of rate constants in organic solvents is not necessarily less challenging than in water and popular solvent models struggle to predict their rate constants to within 3 log units of experimental values. Among the continuum solvent models, the ADF-COSMO-RS model performed the best in predicting absolute rate contants while the SM12 model was best at predicting relative rate constants with an average accuracy of about 1.5 and 0.8 log units, respectively. The use of computationally more demanding MM explicit solvent models did not translate to improvements in absolute rate constants but was quite effective at predicting relative rate constants due to systematic error cancellation. Free energy barriers obtained from umbrella sampling with explicit solvent QM/MM simulations led to excellent agreement with experimental values, provided that a validated level of theory is used to treat the QM region.
Collapse
Affiliation(s)
- Mackenzie Taylor
- School of Chemistry, The University of New South Wales, Sydney, New South Wales2052, Australia
| | - Haibo Yu
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales2522, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales2052, Australia
| |
Collapse
|
6
|
Chen J, Harper JB, Ho J. Improving the Accuracy of Quantum Mechanics/Molecular Mechanics (QM/MM) Models with Polarized Fragment Charges. J Chem Theory Comput 2022; 18:5607-5617. [PMID: 35952004 DOI: 10.1021/acs.jctc.2c00491] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This paper introduces an economical approach for improving the accuracy and convergence of quantum mechanics/molecular mechanics (QM/MM) models. The approach is tested on a series of neutral and charged amino acids embedded in a 160-water cluster, where their intramolecular proton transfer energies (neutral amino acid → zwitterionic amino acid) were previously obtained at the ωB97X-D/6-31G(d) level of theory. When the charges on the MM atoms were replaced with those obtained at the same QM level of theory used to treat the QM atoms, this significantly improved the accuracy and convergence of the QM/MM models. In particular, the QM/MM model converged to within 1.4 kcal mol-1 of directly calculated DFT energies for smaller (by as many as 20 waters) QM regions. The use of atomic charges obtained from the natural population analysis yielded the most significant improvement, while other charge schemes such as Mulliken, electrostatic potential, or CM5 led to poorer outcomes. It is further demonstrated that the QM atomic charges can be accurately estimated in a highly efficient manner using an iterative fragmentation approach based on the moving-domain QM/MM method. Similar observations were made when the approach was used to predict the barrier of an SN2 reaction. Thus, the use of QM-quality atomic charges on MM atoms represents a simple and easy-to-implement strategy for improving the accuracy of QM/MM models.
Collapse
Affiliation(s)
- Junbo Chen
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Jason B Harper
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| | - Junming Ho
- School of Chemistry, The University of New South Wales, Sydney, New South Wales 2052, Australia
| |
Collapse
|
7
|
Peluso P, Chankvetadze B. Recognition in the Domain of Molecular Chirality: From Noncovalent Interactions to Separation of Enantiomers. Chem Rev 2022; 122:13235-13400. [PMID: 35917234 DOI: 10.1021/acs.chemrev.1c00846] [Citation(s) in RCA: 57] [Impact Index Per Article: 28.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
It is not a coincidence that both chirality and noncovalent interactions are ubiquitous in nature and synthetic molecular systems. Noncovalent interactivity between chiral molecules underlies enantioselective recognition as a fundamental phenomenon regulating life and human activities. Thus, noncovalent interactions represent the narrative thread of a fascinating story which goes across several disciplines of medical, chemical, physical, biological, and other natural sciences. This review has been conceived with the awareness that a modern attitude toward molecular chirality and its consequences needs to be founded on multidisciplinary approaches to disclose the molecular basis of essential enantioselective phenomena in the domain of chemical, physical, and life sciences. With the primary aim of discussing this topic in an integrated way, a comprehensive pool of rational and systematic multidisciplinary information is provided, which concerns the fundamentals of chirality, a description of noncovalent interactions, and their implications in enantioselective processes occurring in different contexts. A specific focus is devoted to enantioselection in chromatography and electromigration techniques because of their unique feature as "multistep" processes. A second motivation for writing this review is to make a clear statement about the state of the art, the tools we have at our disposal, and what is still missing to fully understand the mechanisms underlying enantioselective recognition.
Collapse
Affiliation(s)
- Paola Peluso
- Istituto di Chimica Biomolecolare ICB, CNR, Sede secondaria di Sassari, Traversa La Crucca 3, Regione Baldinca, Li Punti, I-07100 Sassari, Italy
| | - Bezhan Chankvetadze
- Institute of Physical and Analytical Chemistry, School of Exact and Natural Sciences, Tbilisi State University, Chavchavadze Avenue 3, 0179 Tbilisi, Georgia
| |
Collapse
|