1
|
Lambros E, Fetherolf JH, Hammes-Schiffer S, Li X. A Many-Body Perspective of Nuclear Quantum Effects in Aqueous Clusters. J Phys Chem Lett 2024; 15:4070-4075. [PMID: 38587257 DOI: 10.1021/acs.jpclett.4c00439] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024]
Abstract
Nuclear quantum effects play an important role in the structure and thermodynamics of aqueous systems. By performing a many-body expansion with nuclear-electronic orbital (NEO) theory, we show that proton quantization can give rise to significant energetic contributions for many-body interactions spanning several molecules in single-point energy calculations of water clusters. Although zero-point motion produces a large increase in energy at the one-body level, nuclear quantum effects serve to stabilize higher-order molecular interactions. These results are significant because they demonstrate that nuclear quantum effects play a nontrivial role in many-body interactions of aqueous systems. Our approach also provides a pathway for incorporating nuclear quantum effects into water potential energy surfaces. The NEO approach is advantageous for many-body expansion analyses because it includes nuclear quantum effects directly in the energies.
Collapse
Affiliation(s)
- Eleftherios Lambros
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Jonathan H Fetherolf
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Sharon Hammes-Schiffer
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Yu Q, Qu C, Houston PL, Nandi A, Pandey P, Conte R, Bowman JM. A Status Report on "Gold Standard" Machine-Learned Potentials for Water. J Phys Chem Lett 2023; 14:8077-8087. [PMID: 37656898 PMCID: PMC10510435 DOI: 10.1021/acs.jpclett.3c01791] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/28/2023] [Indexed: 09/03/2023]
Abstract
Owing to the central importance of water to life as well as its unusual properties, potentials for water have been the subject of extensive research over the past 50 years. Recently, five potentials based on different machine learning approaches have been reported that are at or near the "gold standard" CCSD(T) level of theory. The development of such high-level potentials enables efficient and accurate simulations of water systems using classical and quantum dynamical approaches. This Perspective serves as a status report of these potentials, focusing on their methodology and applications to water systems across different phases. Their performances on the energies of gas phase water clusters, as well as condensed phase structural and dynamical properties, are discussed.
Collapse
Affiliation(s)
- Qi Yu
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent
Researcher, Toronto, Ontario M9B 0E3, Canada
| | - Paul L. Houston
- Department
of Chemistry and Chemical Biology, Cornell
University, Ithaca, New York 14853, United States
- Department of Chemistry
and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Apurba Nandi
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
- Department
of Physics and Materials Science, University
of Luxembourg, L-1511, Luxembourg City, Luxembourg
| | - Priyanka Pandey
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Riccardo Conte
- Dipartimento
di Chimica, Università degli Studi
di Milano, via Golgi 19, 20133 Milano, Italy
| | - Joel M. Bowman
- Department
of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
4
|
Schiltz C, Rappoport D, Mandelshtam VA. Implementation of the self-consistent phonons method with ab initio potentials (AI-SCP). J Chem Phys 2023; 158:2890485. [PMID: 37184023 DOI: 10.1063/5.0146682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 04/24/2023] [Indexed: 05/16/2023] Open
Abstract
The self-consistent phonon (SCP) method allows one to include anharmonic effects when treating a many-body quantum system at thermal equilibrium. The system is then described by an effective temperature-dependent harmonic Hamiltonian, which can be used to estimate its various dynamic and static properties. In this paper, we combine SCP with ab initio (AI) potential energy evaluation in which case the numerical bottleneck of AI-SCP is the evaluation of Gaussian averages of the AI potential energy and its derivatives. These averages are computed efficiently by the quasi-Monte Carlo method utilizing low-discrepancy sequences leading to a fast convergence with respect to the number, S, of the AI energy evaluations. Moreover, a further substantial (an-order-of-magnitude) improvement in efficiency is achieved once a numerically cheap approximation of the AI potential is available. This is based on using a perturbation theory-like (the two-grid) approach in which it is the average of the difference between the AI and the approximate potential that is computed. The corresponding codes and scripts are provided.
Collapse
Affiliation(s)
- Colin Schiltz
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of California, Irvine, California 92697, USA
| | | |
Collapse
|
5
|
Pastorczak M, Duk K, Shahab S, Kananenka AA. Combinational Vibration Modes in H 2O/HDO/D 2O Mixtures Detected Thanks to the Superior Sensitivity of Femtosecond Stimulated Raman Scattering. J Phys Chem B 2023. [PMID: 37201478 DOI: 10.1021/acs.jpcb.3c01334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Overtones and combinational modes frequently play essential roles in ultrafast vibrational energy relaxation in liquid water. However, these modes are very weak and often overlap with fundamental modes, particularly in isotopologues mixtures. We measured VV and HV Raman spectra of H2O and D2O mixtures with femtosecond stimulated Raman scattering (FSRS) and compared the results with calculated spectra. Specifically, we observed the mode at around 1850 cm-1 and assigned it to H-O-D bend + rocking libration. Second, we found that the H-O-D bend overtone band and the OD stretch + rocking libration combination band contribute to the band located between 2850 and 3050 cm-1. Furthermore, we assigned the broad band located between 4000 and 4200 cm-1 to be composed of combinational modes of high-frequency OH stretching modes with predominantly twisting and rocking librations. These results should help in a proper interpretation of Raman spectra of aqueous systems as well as in the identification of vibrational relaxation pathways in isotopically diluted water.
Collapse
Affiliation(s)
- Marcin Pastorczak
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Katsiaryna Duk
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Samaneh Shahab
- Institute of Physical Chemistry, Polish Academy of Sciences, Laser Centre, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Alexei A Kananenka
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
| |
Collapse
|
6
|
Hashim FH, Yu F, Izgorodina EI. Appropriate clusterset selection for the prediction of thermodynamic properties of liquid water with QCE theory. Phys Chem Chem Phys 2023; 25:9846-9858. [PMID: 36945858 DOI: 10.1039/d2cp03712b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
Evident in many physical and chemical phenomena, thermodynamics is the study of how energy is stored, transformed and transferred in a molecule or material. However, prediction of these properties with simulation techniques is a non-trivial task as several factors such as composition and intermolecular interactions come into play. While molecular dynamics and ab initio molecular dynamics are the most common techniques for the prediction of thermodynamic properties, there exists many shortcomings associated with their use. Therefore, in this work we instead apply QCE theory to predict the thermodynamic properties of liquid water. This theory assumes that a condensed phase system can be represented as a 'mixture' of varying sized clusters rather than as a continuum. As QCE theory relies on first-principle simulations and statistical thermodynamics to determine the thermodynamic behavior of a system, appropriate selection of clusters is a crucial step towards achieving accurate predictions. In this study, we use molecular dynamics and ab initio calculations to obtain initial configurations of 400 water clusters, Wn where n = 3 to 10 and contrast their stability using two different criteria. The role of entropy towards cluster stabilization is investigated by comparing the binding (ΔEBIND/mol) and Gibbs free binding energy per molecule (ΔGBIND/mol) of various Wn at 298.15 K. Initial clustersets are constructed by exploring two-, three-, four and five-combinations of clustersets using the minimum ΔGBIND/mol structures of Wn. We also expand the ΔGBIND/mol criteria for Wn of sizes 3 to 7 to include values larger than 0.0 kJ mol-1 and smaller than 3.0 kJ mol-1 as a means of improving thermodynamic predictions. 37 of the 459 resulting clustersets predicted the correct boiling point of water and its thermodynamic properties with an accuracy of 95%. A scaled population-weighted infrared spectrum was compared to experimental results to validate the composition of the top 5 clustersets. The predicted spectra showed an exact match within the low frequency range (<1000 cm-1) with some discrepancy at the high frequency range (>3400 cm-1). This work highlights that ΔGBIND/mol is so far the best criteria to apply when determining an appropriate clusterset for QCE theory.
Collapse
Affiliation(s)
- Fairuz H Hashim
- 17 Rainforest Walk, School of Chemistry, Monash University, Australia.
| | - Fiona Yu
- 17 Rainforest Walk, School of Chemistry, Monash University, Australia.
| | | |
Collapse
|
7
|
Herman KM, Xantheas SS. An extensive assessment of the performance of pairwise and many-body interaction potentials in reproducing ab initio benchmark binding energies for water clusters n = 2-25. Phys Chem Chem Phys 2023; 25:7120-7143. [PMID: 36853239 DOI: 10.1039/d2cp03241d] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We assess the performance of 7 pairwise additive (TIP3P, TIP4P, TIP4P-ice, TIP5P, OPC, SPC, SPC/E) and 8 families of many-body potentials (q-AQUA, HIPPO, AMOEBA, EFP, TTM, WHBB, MB-pol, MB-UCB) in reproducing high-level ab initio benchmark values, CCSD(T) or MP2 at the complete basis set (CBS) limit for the binding energy and the many-body expansion (MBE) of water clusters n = 2-11, 16-17, 20, 25. By including a large range of cluster sizes having dissimilar hydrogen bonding networks, we obtain an understanding of how these potentials perform for different hydrogen bonding arrangements that are mostly outside of their parameterization range. While it is appropriate to compare the results of ab initio based many-body potentials directly to the electronic binding energies (De's), the pairwise additive ones are compared to the enthalpies at T = 298 K, ΔH(298 K), as the latter class of force fields are parametrized to reproduce enthalpies (implicitly accounting for zero-point energy corrections) rather than binding energies. We find that all pairwise additive potentials considered overestimate the reference ΔH values for the n = 2-25 clusters by >13%. For the water dimer (n = 2) in particular, the errors are in the range 83-119% for the pairwise additive potentials studied since these are based on an effective rather than the true 2-body interaction specifically designed as a means of partially accounting for the missing many-body terms. This stronger 2-body interaction is achieved by an enhanced monomer dipole moment that mimics its increase from the gas phase monomer to the condensed phase value. Indeed, for cluster sizes n ≥ 4 the percent deviations become slightly smaller (albeit all exceeding 13%). In contrast, we find that the many-body potentials perform more accurately in reproducing the electronic binding energies (De's) throughout the entire cluster range (n = 2-25), all reproducing the ab initio benchmark binding energies within ±7% of the respective CBS values. We further assess the ability of a subset of the many-body potentials (MB-UCB, q-AQUA, MB-pol, and TTM2.1-F) to also reproduce the magnitude of the ab initio many-body energy terms for water cluster sizes n = 7, 10, 16 and 17. The potentials show an overall good agreement with the available benchmark values. However, we identify characteristic differences upon comparing the many-body terms at both the ab initio-optimized geometries and the respective potential-optimized geometries to the reference ab initio values. Additionally, by applying this analysis to a wide range of cluster sizes, trends in the MBE of the potentials with increasing cluster size can be identified. Finally, in an attempt to draw a parallel between the pairwise additive and many-body potentials, we report the analysis of the individual molecular dipole moments for water clusters with 1 to ∼4 solvation shells with the TTM2.1-F potential. We find that the internally solvated water molecules have in general a larger molecular dipole moment ranging from 2.6-3.0 D. This justifies the use of an enhanced, with respect to the gas-phase value, molecular dipole moment for the pairwise additive potentials, which is intended to fold in the many body terms into an effective (enhanced) pairwise interaction through the choice of the charges. These results have important implications for the development of future generations of efficient, transferable, and highly accurate classical interaction potentials in both the pairwise additive and many-body categories.
Collapse
Affiliation(s)
- Kristina M Herman
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA.
| | - Sotiris S Xantheas
- Department of Chemistry, University of Washington, Seattle, WA 98195, USA. .,Advanced Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, MS K1-83, WA, 99352, USA.
| |
Collapse
|
8
|
Song S, Vuckovic S, Kim Y, Yu H, Sim E, Burke K. Extending density functional theory with near chemical accuracy beyond pure water. Nat Commun 2023; 14:799. [PMID: 36781855 PMCID: PMC9925738 DOI: 10.1038/s41467-023-36094-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 01/13/2023] [Indexed: 02/15/2023] Open
Abstract
Density functional simulations of condensed phase water are typically inaccurate, due to the inaccuracies of approximate functionals. A recent breakthrough showed that the SCAN approximation can yield chemical accuracy for pure water in all its phases, but only when its density is corrected. This is a crucial step toward first-principles biosimulations. However, weak dispersion forces are ubiquitous and play a key role in noncovalent interactions among biomolecules, but are not included in the new approach. Moreover, naïve inclusion of dispersion in HF-SCAN ruins its high accuracy for pure water. Here we show that systematic application of the principles of density-corrected DFT yields a functional (HF-r2SCAN-DC4) which recovers and not only improves over HF-SCAN for pure water, but also captures vital noncovalent interactions in biomolecules, making it suitable for simulations of solutions.
Collapse
Affiliation(s)
- Suhwan Song
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea ,grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA
| | - Stefan Vuckovic
- grid.472716.10000 0004 1758 7362Institute for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy ,grid.12380.380000 0004 1754 9227Departments of Chemistry & Pharmaceutical Sciences and Amsterdam Institute of Molecular and Life Sciences (AIMMS), Faculty of Science, Vrije Universiteit, De Boelelaan 1083, 1081HV Amsterdam, The Netherlands
| | - Youngsam Kim
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Hayoung Yu
- grid.15444.300000 0004 0470 5454Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722 Korea
| | - Eunji Sim
- Department of Chemistry, Yonsei University, 50 Yonsei-ro Seodaemun-gu, Seoul, 03722, Korea.
| | - Kieron Burke
- grid.266093.80000 0001 0668 7243Department of Chemistry, University of California, Irvine, CA 92697 USA ,grid.266093.80000 0001 0668 7243Departments of Physics & Astronomy, University of California, Irvine, CA 92697 USA
| |
Collapse
|
9
|
Bowman JM, Qu C, Conte R, Nandi A, Houston PL, Yu Q. Δ-Machine Learned Potential Energy Surfaces and Force Fields. J Chem Theory Comput 2023; 19:1-17. [PMID: 36527383 DOI: 10.1021/acs.jctc.2c01034] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
There has been great progress in developing machine-learned potential energy surfaces (PESs) for molecules and clusters with more than 10 atoms. Unfortunately, this number of atoms generally limits the level of electronic structure theory to less than the "gold standard" CCSD(T) level. Indeed, for the well-known MD17 dataset for molecules with 9-20 atoms, all of the energies and forces were obtained with DFT calculations (PBE). This Perspective is focused on a Δ-machine learning method that we recently proposed and applied to bring DFT-based PESs to close to CCSD(T) accuracy. This is demonstrated for hydronium, N-methylacetamide, acetyl acetone, and ethanol. For 15-atom tropolone, it appears that special approaches (e.g., molecular tailoring, local CCSD(T)) are needed to obtain the CCSD(T) energies. A new aspect of this approach is the extension of Δ-machine learning to force fields. The approach is based on many-body corrections to polarizable force field potentials. This is examined in detail using the TTM2.1 water potential. The corrections make use of our recent CCSD(T) datasets for 2-b, 3-b, and 4-b interactions for water. These datasets were used to develop a new fully ab initio potential for water, termed q-AQUA.
Collapse
Affiliation(s)
- Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Chen Qu
- Independent Researcher, Toronto, Canada 66777
| | - Riccardo Conte
- Dipartimento di Chimica, Università Degli Studi di Milano, via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States.,Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| |
Collapse
|
10
|
Jónsson EÖ, Rasti S, Galynska M, Meyer J, Jónsson H. Transferable Potential Function for Flexible H 2O Molecules Based on the Single-Center Multipole Expansion. J Chem Theory Comput 2022; 18:7528-7543. [PMID: 36395502 DOI: 10.1021/acs.jctc.2c00598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
A potential function is presented for describing a system of flexible H2O molecules based on the single-center multipole expansion (SCME) of the electrostatic interaction. The model, referred to as SCME/f, includes the variation of the molecular quadrupole moment as well as the dipole moment with changes in bond length and angle so as to reproduce results of high-level electronic structure calculations. The multipole expansion also includes fixed octupole and hexadecapole moments, as well as anisotropic dipole-dipole, dipole-quadrupole, and quadrupole-quadrupole polarizability tensors. The model contains five adjustable parameters related to the repulsive interaction and damping functions in the electrostatic and dispersion interactions. Their values are adjusted to reproduce the lowest energy isomers of small clusters, (H2O)n with n = 2-6, as well as measured properties of the ice Ih crystal. Subsequent calculations of the energy difference between the various isomer configurations of the clusters show that SCME/f gives good agreement with results of electronic structure calculations and represents a significant improvement over the previously presented rigid SCME potential function. Analysis of the vibrational frequencies of the clusters and structural properties of ice Ih crystal show the importance of accurately describing the variation of the quadrupole moment with molecular structures.
Collapse
Affiliation(s)
- Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Soroush Rasti
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Marta Galynska
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| | - Jörg Meyer
- Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, 2300 RALeiden, The Netherlands
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences, University of Iceland, VR-III, 107Reykjavík, Iceland
| |
Collapse
|
11
|
Mauger N, Plé T, Lagardère L, Huppert S, Piquemal JP. Improving Condensed-Phase Water Dynamics with Explicit Nuclear Quantum Effects: The Polarizable Q-AMOEBA Force Field. J Phys Chem B 2022; 126:8813-8826. [PMID: 36270033 DOI: 10.1021/acs.jpcb.2c04454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
We introduce a new parametrization of the AMOEBA polarizable force field for water denoted Q-AMOEBA, for use in simulations that explicitly account for nuclear quantum effects (NQEs). This study is made possible thanks to the recently introduced adaptive Quantum Thermal Bath (adQTB) simulation technique which computational cost is comparable to classical molecular dynamics. The flexible Q-AMOEBA model conserves the initial AMOEBA functional form, with an intermolecular potential including an atomic multipole description of electrostatic interactions (up to quadrupole), a polarization contribution based on the Thole interaction model and a buffered 14-7 potential to model van der Waals interactions. It has been obtained by using a ForceBalance fitting strategy including high-level quantum chemistry reference energies and selected condensed-phase properties targets. The final Q-AMOEBA model is shown to accurately reproduce both gas-phase and condensed-phase properties, notably improving the original AMOEBA water model. This development allows the fine study of NQEs on water liquid phase properties such as the average H-O-H angle compared to its gas-phase equilibrium value, isotope effects, and so on. Q-AMOEBA also provides improved infrared spectroscopy prediction capabilities compared to AMOEBA03. Overall, we show that the impact of NQEs depends on the underlying model functional form and on the associated strength of hydrogen bonds. Since adQTB simulations can be performed at near classical computational cost using the Tinker-HP package, Q-AMOEBA can be extended to organic molecules, proteins, and nucleic acids opening the possibility for the large-scale study of the importance of NQEs in biophysics.
Collapse
Affiliation(s)
- Nastasia Mauger
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Thomas Plé
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Louis Lagardère
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| | - Simon Huppert
- Sorbonne Université, Institut des NanoSciences de Paris, UMR 7588 CNRS, 75005 Paris, France
| | - Jean-Philip Piquemal
- Sorbonne Université, Laboratoire de Chimie Théorique, UMR 7616 CNRS, 75005 Paris, France
| |
Collapse
|
12
|
Effect of Orientational Isomerism in Neutral Water Hexamers on Their Thermodynamic Properties and Concentrations in the Gas Phase. J CLUST SCI 2022. [DOI: 10.1007/s10876-022-02365-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
13
|
Jana S, Constantin LA, Smiga S, Samal P. Solid-state performance of a meta-GGA screened hybrid density functional constructed from Pauli kinetic enhancement factor dependent semilocal exchange hole. J Chem Phys 2022; 157:024102. [DOI: 10.1063/5.0096674] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The semilocal form of the exchange hole is highly useful in developing non-local range-separated hybrid density functionals for finite and extended systems. The way to construct the conventional exact exchange hole model is based on either the Taylor series expansion or the reverse engineering technique from the corresponding exchange energy functional. Although the latter technique is quite popular in context of generalized gradient approximation (GGA) functionals, the same for the meta-GGA functionals is not so much explored. Thus, in this study, we propose a reverse-engineered semilocal exchange hole of a meta-GGA functional, that depends only on the meta-GGA ingredient α (also known as the Pauli kinetic energy enhancement factor). The model is used subsequently to design the short-range-separated meta-GGA hybrid density functional. We show that the present method can be successfully applied for several challenging problems in the context of solids, especially for which the GGA based hybrid fails drastically. This assessment proves that the present functional is quite useful for materials sciences. Finally, we also use this method for several molecular test cases, where the results are also as comparative as its base semilocal functional.
Collapse
Affiliation(s)
- Subrata Jana
- Department of Chemistry and Biochemistry, The Ohio State University, United States of America
| | - Lucian A. Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy, Italy
| | - Szymon Smiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University Institute of Physics, Poland
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, India
| |
Collapse
|
14
|
Naseem-Khan S, Lagardère L, Narth C, Cisneros GA, Ren P, Gresh N, Piquemal JP. Development of the Quantum-Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed-Phase Molecular Dynamics Simulations. J Chem Theory Comput 2022; 18:3607-3621. [PMID: 35575306 PMCID: PMC10851344 DOI: 10.1021/acs.jctc.2c00029] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We present the extension of the Sum of Interactions Between Fragments Ab initio Computed (SIBFA) many-body polarizable force field to condensed-phase molecular dynamics (MD) simulations. The quantum-inspired SIBFA procedure is grounded on simplified integrals obtained from localized molecular orbital theory and achieves full separability of its intermolecular potential. It embodies long-range multipolar electrostatics (up to quadrupole) coupled to a short-range penetration correction (up to charge-quadrupole), exchange repulsion, many-body polarization, many-body charge transfer/delocalization, exchange dispersion, and dispersion (up to C10). This enables the reproduction of all energy contributions of ab initio symmetry-adapted perturbation theory (SAPT(DFT)) gas-phase reference computations. The SIBFA approach has been integrated within the Tinker-HP massively parallel MD package. To do so, all SIBFA energy gradients have been derived and the approach has been extended to enable periodic boundary conditions simulations using smooth particle mesh Ewald. This novel implementation also notably includes a computationally tractable simplification of the many-body charge transfer/delocalization contribution. As a proof of concept, we perform a first computational experiment defining a water model fitted on a limited set of SAPT(DFT) data. SIBFA is shown to enable a satisfactory reproduction of both gas-phase energetic contributions and condensed-phase properties highlighting the importance of its physically motivated functional form.
Collapse
Affiliation(s)
- Sehr Naseem-Khan
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Louis Lagardère
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- IP2CT, FR 2622, CNRS, Sorbonne Université, 75005 Paris, France
| | | | - G Andrés Cisneros
- Department of Chemistry, University of North Texas, Denton, Texas 76201, United States
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Nohad Gresh
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
| | - Jean-Philip Piquemal
- LCT, UMR 7616 CNRS, Sorbonne Université, 75005 Paris, France
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, Texas 78712, United States
- Institut Universitaire de France, 75005 Paris, France
| |
Collapse
|
15
|
Yu Q, Qu C, Houston PL, Conte R, Nandi A, Bowman JM. q-AQUA: A Many-Body CCSD(T) Water Potential, Including Four-Body Interactions, Demonstrates the Quantum Nature of Water from Clusters to the Liquid Phase. J Phys Chem Lett 2022; 13:5068-5074. [PMID: 35652912 DOI: 10.1021/acs.jpclett.2c00966] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Many model potential energy surfaces (PESs) have been reported for water; however, none are strictly from "first-principles". Here we report such a potential, based on a many-body representation at the CCSD(T) level of theory up to the four-body interaction. The new PES is benchmarked for the isomers of the water hexamer for dissociation energies, harmonic frequencies, and unrestricted diffusion Monte Carlo (DMC) calculations of the zero-point energies of the Prism, Book, and Cage isomers. Dissociation energies of several isomers of the 20-mer agree well with recent benchmark energies. Exploratory DMC calculations on this cluster verify the robustness of the new PES for quantum simulations. The accuracy and speed of the new PES are demonstrated for standard condensed phase properties, i.e., the radial distribution function and the self-diffusion constant. Quantum effects are shown to be substantial for these observables and also needed to bring theory into excellent agreement with experiment.
Collapse
Affiliation(s)
- Qi Yu
- Department of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Chen Qu
- Independent Researcher, Toronto, Ontario, Canada
| | - Paul L Houston
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
- Department of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Riccardo Conte
- Dipartimento di Chimica, Università degli Studi di Milano, Via Golgi 19, 20133 Milano, Italy
| | - Apurba Nandi
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| | - Joel M Bowman
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, United States
| |
Collapse
|
16
|
Rackers JA, Silva RR, Wang Z, Ponder JW. Polarizable Water Potential Derived from a Model Electron Density. J Chem Theory Comput 2021; 17:7056-7084. [PMID: 34699197 DOI: 10.1021/acs.jctc.1c00628] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A new empirical potential for efficient, large scale molecular dynamics simulation of water is presented. The HIPPO (Hydrogen-like Intermolecular Polarizable POtential) force field is based upon the model electron density of a hydrogen-like atom. This framework is used to derive and parametrize individual terms describing charge penetration damped permanent electrostatics, damped polarization, charge transfer, anisotropic Pauli repulsion, and damped dispersion interactions. Initial parameter values were fit to Symmetry Adapted Perturbation Theory (SAPT) energy components for ten water dimer configurations, as well as the radial and angular dependence of the canonical dimer. The SAPT-based parameters were then systematically refined to extend the treatment to water bulk phases. The final HIPPO water model provides a balanced representation of a wide variety of properties of gas phase clusters, liquid water, and ice polymorphs, across a range of temperatures and pressures. This water potential yields a rationalization of water structure, dynamics, and thermodynamics explicitly correlated with an ab initio energy decomposition, while providing a level of accuracy comparable or superior to previous polarizable atomic multipole force fields. The HIPPO water model serves as a cornerstone around which similarly detailed physics-based models can be developed for additional molecular species.
Collapse
Affiliation(s)
- Joshua A Rackers
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States.,Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico 87123, United States
| | - Roseane R Silva
- Program in Computational & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Zhi Wang
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States
| | - Jay W Ponder
- Department of Chemistry, Washington University in Saint Louis, Saint Louis, Missouri 63130, United States.,Department of Biochemistry & Molecular Biophysics, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| |
Collapse
|
17
|
Malloum A, Conradie J. Hydrogen bond networks of ammonia clusters: What we know and what we don’t know. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
|
18
|
Louisnard F, Geudtner G, Köster AM, Cuny J. Implementation of the parallel-tempering molecular dynamics method in deMon2k and application to the water hexamer. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02765-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
19
|
Malloum A, Conradie J. Structures of water clusters in the solvent phase and relative stability compared to gas phase. Polyhedron 2021. [DOI: 10.1016/j.poly.2020.114856] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
|
20
|
Jana S, Patra A, Śmiga S, Constantin LA, Samal P. Insights from the density functional performance of water and water–solid interactions: SCAN in relation to other meta-GGAs. J Chem Phys 2020; 153:214116. [DOI: 10.1063/5.0028821] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Abhilash Patra
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Szymon Śmiga
- Institute of Physics, Faculty of Physics, Astronomy and Informatics, Nicolaus Copernicus University, Grudziadzka 5, 87-100 Toruń, Poland
| | - Lucian A. Constantin
- Istituto di Nanoscienze, Consiglio Nazionale delle Ricerche CNR-NANO, 41125 Modena, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| |
Collapse
|
21
|
|
22
|
Lee VGM, Vetterli NJ, Boyer MA, McCoy AB. Diffusion Monte Carlo Studies on the Detection of Structural Changes in the Water Hexamer upon Isotopic Substitution. J Phys Chem A 2020; 124:6903-6912. [DOI: 10.1021/acs.jpca.0c05686] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Victor G. M. Lee
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Nicholas J. Vetterli
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Mark A. Boyer
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Anne B. McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
23
|
Ricard TC, Iyengar SS. Efficient and Accurate Approach To Estimate Hybrid Functional and Large Basis-Set Contributions to Condensed-Phase Systems and Molecule–Surface Interactions. J Chem Theory Comput 2020; 16:4790-4812. [DOI: 10.1021/acs.jctc.9b01089] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Timothy C. Ricard
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Srinivasan S. Iyengar
- Department of Chemistry and Department of Physics, Indiana University, 800 E. Kirkwood Avenue, Bloomington, Indiana 47405, United States
| |
Collapse
|
24
|
Self-interaction error overbinds water clusters but cancels in structural energy differences. Proc Natl Acad Sci U S A 2020; 117:11283-11288. [PMID: 32393631 DOI: 10.1073/pnas.1921258117] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We gauge the importance of self-interaction errors in density functional approximations (DFAs) for the case of water clusters. To this end, we used the Fermi-Löwdin orbital self-interaction correction method (FLOSIC) to calculate the binding energy of clusters of up to eight water molecules. Three representative DFAs of the local, generalized gradient, and metageneralized gradient families [i.e., local density approximation (LDA), Perdew-Burke-Ernzerhof (PBE), and strongly constrained and appropriately normed (SCAN)] were used. We find that the overbinding of the water clusters in these approximations is not a density-driven error. We show that, while removing self-interaction error does not alter the energetic ordering of the different water isomers with respect to the uncorrected DFAs, the resulting binding energies are corrected toward accurate reference values from higher-level calculations. In particular, self-interaction-corrected SCAN not only retains the correct energetic ordering for water hexamers but also reduces the mean error in the hexamer binding energies to less than 14 meV/[Formula: see text] from about 42 meV/[Formula: see text] for SCAN. By decomposing the total binding energy into many-body components, we find that large errors in the two-body interaction in SCAN are significantly reduced by self-interaction corrections. Higher-order many-body errors are small in both SCAN and self-interaction-corrected SCAN. These results indicate that orbital-by-orbital removal of self-interaction combined with a proper DFA can lead to improved descriptions of water complexes.
Collapse
|
25
|
Wan Z, Wang QD. Accurate prediction of enthalpy of formation combined with AM1 method and molecular descriptors. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137327] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
26
|
Zhao CL, Zhao DX, Jiang QY, Zhang HX, Li S, Yang ZZ. Polarizable TIP7P Water Model with Perturbation Charges Evaluated from ABEEM. J Phys Chem B 2020; 124:2450-2464. [PMID: 32141292 DOI: 10.1021/acs.jpcb.9b11775] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A polarizable version of the rigid seven-site (TIP7P) water model with the atom-bond electronegativity equalization method (ABEEM) is proposed. The model uses direct polarization, where an isolated water monomer in the equilibrium geometry is assumed as a reference state and the polarization of the monomer arises from interacting with other molecules as a perturbation of the reference state. The charge on each site of the monomer splits into reference charge and perturbation charge. The perturbation charge arises only because of other reference charges. The interaction of the perturbation charge with other perturbation charges is replaced using polarization scaling to enhance the interaction of perturbation charge with the reference charges of the sites from other molecules. The perturbation charges are updated by evaluating explicit expressions once. This direct polarization is time-reversible because the charge update is independent of the charges in previous simulation steps. A Slater-type damping function moderates the short-range electrostatics to treat charge diffusion. The Ewald method corrects the long-range electrostatics both in the nuclei movement and in electronegativity equalization to diminish the size effect. The water model is parameterized by fitting the ab initio results of water clusters and the experimental results of water monomers and thermodynamic properties for liquid water. Owing to polarizability, the model performs better than the TIP7P model in terms of vaporization enthalpy, isothermal compressibility, and shear viscosity of the liquid phase. It performs better at the melting point of ice but slightly worse under critical conditions than the TIP7P model. Direct polarization has a low time complexity of O(N) and is a good choice for ABEEM to improve its computational efficiency.
Collapse
Affiliation(s)
- Chong-Li Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Dong-Xia Zhao
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Qian-Ying Jiang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Hai-Xia Zhang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| | - Shenmin Li
- College of Environment and Chemical Engineering, Dalian University, Dalian 116622, People's Republic of China
| | - Zhong-Zhi Yang
- School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian 116029, People's Republic of China
| |
Collapse
|
27
|
Gilmore RAJ, Dove MT, Misquitta AJ. First-Principles Many-Body Nonadditive Polarization Energies from Monomer and Dimer Calculations Only: A Case Study on Water. J Chem Theory Comput 2020; 16:224-242. [PMID: 31769980 DOI: 10.1021/acs.jctc.9b00819] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The many-body polarization energy is the major source of nonadditivity in strongly polar systems such as water. This nonadditivity is often considerable and must be included, if only in an average manner, to correctly describe the physical properties of the system. Models for the polarization energy are usually parametrized using experimental data, or theoretical estimates of the many-body effects. Here we show how many-body polarization models can be developed for water complexes using data for the monomer and dimer only using ideas recently developed in the field of intermolecular perturbation theory and state-of-the-art approaches for calculating distributed molecular properties based on the iterated stockholder atoms (ISA) algorithm. We show how these models can be calculated, and we validate their accuracy in describing the many-body nonadditive energies of a range of water clusters. We further investigate their sensitivity to the details of the polarization damping models used. We show how our very best polarization models yield many-body energies that agree with those computed with coupled-cluster methods, but at a fraction of the computational cost.
Collapse
Affiliation(s)
- Rory A J Gilmore
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
| | - Martin T Dove
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
| | - Alston J Misquitta
- School of Physics and Astronomy and the Thomas Young Centre for Theory and Simulation of Materials at Queen Mary University of London , London E1 4NS , U.K
| |
Collapse
|
28
|
Jana S, Constantin LA, Samal P. Accurate Water Properties from an Efficient ab Initio Method. J Chem Theory Comput 2020; 16:974-987. [DOI: 10.1021/acs.jctc.9b01018] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Lucian A. Constantin
- Center for Biomolecular Nanotechnologies @UNILE, Istituto Italiano di Tecnologia, Via Barsanti, I-73010 Arnesano, Italy
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| |
Collapse
|
29
|
Dohn AO, Jónsson EÖ, Jónsson H. Polarizable Embedding with a Transferable H 2O Potential Function II: Application to (H 2O) n Clusters and Liquid Water. J Chem Theory Comput 2019; 15:6578-6587. [PMID: 31692344 DOI: 10.1021/acs.jctc.9b00778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The incorporation of polarization in multiscale quantum-mechanics/molecular-mechanics (QM/MM) simulations is important for a variety of applications, for example, charge-transfer reactions. A recently developed formalism based on a density functional theory description of the QM region and a potential energy function for H2O molecules that includes quadrupole as well as dipole polarizability of the MM region is used to simulate liquid water and water clusters. Analysis of the energy, atomic forces, MM polarization, and structure is presented. A quantitative assessment of the QM/MM-MM/MM interaction energy differences of all possible QM/MM configurations of (H2O)n clusters shows that the interquartile range of the distributions of the QM/MM binding energies is never more than 20 meV/molecule higher or lower than the binding energies produced with either of the single-model results. Comparing these interaction energy differences with the QM/MM induction differences show that they are not systematically caused by the induced MM moments of our polarizable embedding scheme. Optimized hexamer geometries as well as the liquid water structure are shown to be improved in comparison with results obtained using point-charge based embedding models neglecting polarization.
Collapse
Affiliation(s)
- Asmus Ougaard Dohn
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
| | - Elvar Örn Jónsson
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
| | - Hannes Jónsson
- Science Institute and Faculty of Physical Sciences , University of Iceland , Reykjavík 107 , Iceland
| |
Collapse
|
30
|
Patkowski K. Recent developments in symmetry‐adapted perturbation theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1452] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Konrad Patkowski
- Department of Chemistry and Biochemistry Auburn University Auburn Alabama
| |
Collapse
|
31
|
Abstract
Since the introduction of the fragment molecular orbital method 20 years ago, fragment-based approaches have occupied a small but growing niche in quantum chemistry. These methods decompose a large molecular system into subsystems small enough to be amenable to electronic structure calculations, following which the subsystem information is reassembled in order to approximate an otherwise intractable supersystem calculation. Fragmentation sidesteps the steep rise (with respect to system size) in the cost of ab initio calculations, replacing it with a distributed cost across numerous computer processors. Such methods are attractive, in part, because they are easily parallelizable and therefore readily amenable to exascale computing. As such, there has been hope that distributed computing might offer the proverbial "free lunch" in quantum chemistry, with the entrée being high-level calculations on very large systems. While fragment-based quantum chemistry can count many success stories, there also exists a seedy underbelly of rarely acknowledged problems. As these methods begin to mature, it is time to have a serious conversation about what they can and cannot be expected to accomplish in the near future. Both successes and challenges are highlighted in this Perspective.
Collapse
Affiliation(s)
- John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
32
|
Das AK, Urban L, Leven I, Loipersberger M, Aldossary A, Head-Gordon M, Head-Gordon T. Development of an Advanced Force Field for Water Using Variational Energy Decomposition Analysis. J Chem Theory Comput 2019; 15:5001-5013. [DOI: 10.1021/acs.jctc.9b00478] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
|
33
|
Riera M, Lambros E, Nguyen TT, Götz AW, Paesani F. Low-order many-body interactions determine the local structure of liquid water. Chem Sci 2019; 10:8211-8218. [PMID: 32133122 PMCID: PMC6927411 DOI: 10.1039/c9sc03291f] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 07/21/2019] [Indexed: 12/30/2022] Open
Abstract
Two-body and three-body energies, modulated by higher-body terms and nuclear quantum effects, determine the structure of liquid water and require sub-chemical accuracy that is achieved by the MB-pol model but not by existing DFT functionals.
Despite its apparent simplicity, water displays unique behavior across the phase diagram which is strictly related to the ability of the water molecules to form dense, yet dynamic, hydrogen-bond networks that continually fluctuate in time and space. The competition between different local hydrogen-bonding environments has been hypothesized as a possible origin of the anomalous properties of liquid water. Through a systematic application of the many-body expansion of the total energy, we demonstrate that the local structure of liquid water at room temperature is determined by a delicate balance between two-body and three-body energies, which is further modulated by higher-order many-body effects. Besides providing fundamental insights into the structure of liquid water, this analysis also emphasizes that a correct representation of two-body and three-body energies requires sub-chemical accuracy that is nowadays only achieved by many-body models rigorously derived from the many-body expansion of the total energy, which thus hold great promise for shedding light on the molecular origin of the anomalous behavior of liquid water.
Collapse
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Eleftherios Lambros
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Thuong T Nguyen
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA
| | - Andreas W Götz
- San Diego Supercomputer Center , University of California , San Diego , La Jolla , California 92093 , USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry , University of California , San Diego , La Jolla , California 92093 , USA.,San Diego Supercomputer Center , University of California , San Diego , La Jolla , California 92093 , USA.,Materials Science and Engineering , University of California , San Diego , La Jolla , California 92093 , USA .
| |
Collapse
|
34
|
Liu C, Piquemal JP, Ren P. AMOEBA+ Classical Potential for Modeling Molecular Interactions. J Chem Theory Comput 2019; 15:4122-4139. [PMID: 31136175 DOI: 10.1021/acs.jctc.9b00261] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Classical potentials based on isotropic and additive atomic charges have been widely used to model molecules in computers for the past few decades. The crude approximations in the underlying physics are hindering both their accuracy and transferability across chemical and physical environments. Here we present a new classical potential, AMOEBA+, to capture essential intermolecular forces, including permanent electrostatics, repulsion, dispersion, many-body polarization, short-range charge penetration, and charge transfer, by extending the polarizable multipole-based AMOEBA (Atomic Multipole Optimized Energetics for Biomolecular Applications) model. For a set of common organic molecules, we show that AMOEBA+ with general parameters can reproduce both quantum mechanical interactions and energy decompositions according to Symmetry-Adapted Perturbation Theory (SAPT). Additionally, a new water model based on the AMOEBA+ framework captures various liquid-phase properties in molecular dynamics simulations while remaining consistent with SAPT energy decompositions, utilizing both ab initio data and experimental liquid properties. Our results demonstrate that it is possible to improve the physical basis of classical force fields to advance their accuracy and general applicability.
Collapse
Affiliation(s)
- Chengwen Liu
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| | - Jean-Philip Piquemal
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States.,Laboratoire de Chimie Théorique , Sorbonne Université, UMR7616 CNRS , Paris 75252 , France.,Institut Universitaire de France , Paris Cedex 05, 75005 , France
| | - Pengyu Ren
- Department of Biomedical Engineering , The University of Texas at Austin , Austin , Texas 78712 , United States
| |
Collapse
|
35
|
Yang L, Ji H, Liu X, Lu W. Ring-Stacking Water Clusters: Morphology and Stabilities. ChemistryOpen 2019; 8:210-218. [PMID: 30815330 PMCID: PMC6376211 DOI: 10.1002/open.201800284] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/16/2019] [Indexed: 12/12/2022] Open
Abstract
The structures and interaction energies of water clusters with ring stacking motifs are studied by using ab initio calculations. The structures of the water clusters are constructed by stacking either single rings or multi-rings of tetramer, pentamer, and hexamer. We found that, in the single-ring-stacking motif, the most stable isomers exhibit an alternative clockwise-anticlockwise stacking pattern. We also show that four-layer single-ring-stacking isomers are not energetically favorable in comparison with those of two-layer multi-ring-stacking isomers. The relative stability of the isomers is also analyzed in terms of H-bond strength and elastic distortions of the water molecules.
Collapse
Affiliation(s)
- Liu Yang
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
| | - Hanyang Ji
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
| | - Xiaojie Liu
- Center for Quantum Sciences and School of PhysicsNortheast Normal UniversityChangchun130117China
- Center for Advanced Optoelectronic Functional Materials Research and Key Laboratory of UV Light-Emitting Materials and Technology of Ministry of EducationsNortheast Normal UniversityChangchun130024China
| | - Wen‐Cai Lu
- State Key Laboratory of Theoretical and Computational Chemistry Institute of Theoretical ChemistryJilin University ChangchunJilin130021PR China
| |
Collapse
|
36
|
Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Conradie J. Structures, relative stability and binding energies of neutral water clusters, (H2O)2–30. NEW J CHEM 2019. [DOI: 10.1039/c9nj01659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have revised the structures of neutral water clusters, (H2O)n=2–30, with the affordable M06-2X functional, presenting up to 25 isomers for each cluster size.
Collapse
Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
| |
Collapse
|
37
|
Ougaard Dohn A, Selli D, Fazio G, Ferraro L, Mortensen JJ, Civalleri B, Di Valentin C. Interfacing CRYSTAL/AMBER to Optimize QM/MM Lennard⁻Jones Parameters for Water and to Study Solvation of TiO₂ Nanoparticles. Molecules 2018; 23:molecules23112958. [PMID: 30428551 PMCID: PMC6278561 DOI: 10.3390/molecules23112958] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 11/01/2018] [Accepted: 11/06/2018] [Indexed: 11/28/2022] Open
Abstract
Metal oxide nanoparticles (NPs) are regarded as good candidates for many technological applications, where their functional environment is often an aqueous solution. The correct description of metal oxide electronic structure is still a challenge for local and semilocal density functionals, whereas hybrid functional methods provide an improved description, and local atomic function-based codes such as CRYSTAL17 outperform plane wave codes when it comes to hybrid functional calculations. However, the computational cost of hybrids are still prohibitive for systems of real sizes, in a real environment. Therefore, we here present and critically assess the accuracy of our electrostatic embedding quantum mechanical/molecular mechanical (QM/MM) coupling between CRYSTAL17 and AMBER16, and demonstrate some of its capabilities via the case study of TiO2 NPs in water. First, we produced new Lennard–Jones (LJ) parameters that improve the accuracy of water–water interactions in the B3LYP/TIP3P coupling. We found that optimizing LJ parameters based on water tri- to deca-mer clusters provides a less overstructured QM/MM liquid water description than when fitting LJ parameters only based on the water dimer. Then, we applied our QM/MM coupling methodology to describe the interaction of a 1 nm wide multilayer of water surrounding a spherical TiO2 nanoparticle (NP). Optimizing the QM/MM water–water parameters was found to have little to no effect on the local NP properties, which provide insights into the range of influence that can be attributed to the LJ term in the QM/MM coupling. The effect of adding additional water in an MM fashion on the geometry optimized nanoparticle structure is small, but more evident effects are seen in its electronic properties. We also show that there is good transferability of existing QM/MM LJ parameters for organic molecules–water interactions to our QM/MM implementation, even though these parameters were obtained with a different QM code and QM/MM implementation, but with the same functional.
Collapse
Affiliation(s)
- Asmus Ougaard Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland, 107 Reykjavík, Iceland.
| | - Daniele Selli
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Gianluca Fazio
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Lorenzo Ferraro
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| | - Jens Jørgen Mortensen
- CAMD, Department of Physics, Technical University of Denmark, 2800 Kongens Lyngby, Denmark.
| | - Bartolomeo Civalleri
- Dipartimento di Chimica, Università di Torino and NIS Centre of Excellence, Via P. Giuria 7, I-10129 Torino, Italy.
| | - Cristiana Di Valentin
- Dipartimento di Scienza dei Materiali, Università di Milano-Bicocca, via Cozzi 55, 20125 Milano, Italy.
| |
Collapse
|
38
|
Cole WTS, Yönder Ö, Sheikh AA, Fellers RS, Viant MR, Saykally RJ, Farrell JD, Wales DJ. Terahertz VRT Spectroscopy of the Water Hexamer-h12 Cage: Dramatic Libration-Induced Enhancement of Hydrogen Bond Tunneling Dynamics. J Phys Chem A 2018; 122:7421-7426. [PMID: 30148958 DOI: 10.1021/acs.jpca.8b05777] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the assignment and analysis of 176 transitions belonging to a librational band of the (H2O)6 cage isomer near 525 cm-1(15 THz). From a fit of the transitions to an asymmetric top model, we observe both dramatic changes in the rotational constants relative to the ground state, indicating significant nonrigidity, and striking enhancement in the tunneling motions that break and reform the hydrogen bonds in the cluster. This is the fifth water cluster system to display such an enhancement in the 15 THz librational region, the details of which may help to elucidate the hydrogen bond dynamics occurring in bulk liquid water.
Collapse
Affiliation(s)
- William T S Cole
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Özlem Yönder
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Lehrstuhl für Theoretische Chemie , Ruhr-Universität Bochum , D-44780 Bochum , North Rhine-Westphalia Germany
| | - Akber A Sheikh
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Raymond S Fellers
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Mark R Viant
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - Richard J Saykally
- Department of Chemistry , University of California , Berkeley , California 94720 , United States
| | - James D Farrell
- CAS Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China
| | - David J Wales
- CAS Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics , Institute of Physics, Chinese Academy of Sciences , Beijing 100190 , China.,Department of Chemistry , University of Cambridge , Cambridge CB2 1EW , U.K
| |
Collapse
|
39
|
Nguyen TT, Székely E, Imbalzano G, Behler J, Csányi G, Ceriotti M, Götz AW, Paesani F. Comparison of permutationally invariant polynomials, neural networks, and Gaussian approximation potentials in representing water interactions through many-body expansions. J Chem Phys 2018; 148:241725. [DOI: 10.1063/1.5024577] [Citation(s) in RCA: 118] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Thuong T. Nguyen
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Eszter Székely
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Giulio Imbalzano
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Jörg Behler
- Universität Göttingen, Institut für Physikalische Chemie, Theoretische Chemie, Tammannstr. 6, 37077 Göttingen, Germany
| | - Gábor Csányi
- Engineering Department, University of Cambridge, Trumpington Street, Cambridge CB2 1PZ, United Kingdom
| | - Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Andreas W. Götz
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093, USA
- San Diego Supercomputer Center, University of California, San Diego, La Jolla, California 92093, USA
| |
Collapse
|
40
|
Heßelmann A. Correlation effects and many-body interactions in water clusters. Beilstein J Org Chem 2018; 14:979-991. [PMID: 29977369 PMCID: PMC6009095 DOI: 10.3762/bjoc.14.83] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 04/11/2018] [Indexed: 11/23/2022] Open
Abstract
Background: The quantum-chemical description of the interactions in water clusters is an essential basis for deriving accurate and physically sound models of the interaction potential for water to be used in molecular simulations. In particular, the role of many-body interactions beyond the two-body interactions, which are often not explicitly taken into account by empirical force fields, can be accurately described by quantum chemistry methods on an adequate level, e.g., random-phase approximation electron correlation methods. The relative magnitudes of the different interaction energy contributions obtained by accurate ab initio calculations can therefore provide useful insights that can be exploited to develop enhanced force field methods. Results: In line with earlier theoretical studies of the interactions in water clusters, it has been found that the main contribution to the many-body interactions in clusters with a size of up to N = 13 molecules are higher-order polarisation interaction terms. Compared to this, many-body dispersion interactions are practically negligible for all studied sytems. The two-body dispersion interaction, however, plays a significant role in the formation of the structures of the water clusters and their stability, since it leads to a distinct compression of the cluster sizes compared to the structures optimized on an uncorrelated level. Overall, the many-body interactions amount to about 13% of the total interaction energy, irrespective of the cluster size. The electron correlation contribution to these, however, amounts to only about 30% to the total many-body interactions for the largest clusters studied and is repulsive for all structures considered in this work. Conclusion: While this shows that three- and higher-body interactions can not be neglected in the description of water complexes, the electron correlation contributions to these are much smaller in comparison to the two-body electron correlation effects. Efficient quantum chemistry approaches for describing intermolecular interactions between water molecules may therefore describe higher-body interactions on an uncorrelated Hartree-Fock level without a serious loss in accuracy.
Collapse
Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, 91058 Erlangen, Germany
| |
Collapse
|
41
|
Affiliation(s)
- Kazuaki Kuwahata
- Department of Physics; Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku; Yokohama 240-8501 Japan
| | - Kaoru Ohno
- Department of Physics; Yokohama National University, 79-5 Tokiwadai, Hodogaya-ku; Yokohama 240-8501 Japan
| |
Collapse
|
42
|
Richard RM, Bakr BW, Sherrill CD. Understanding the Many-Body Basis Set Superposition Error: Beyond Boys and Bernardi. J Chem Theory Comput 2018; 14:2386-2400. [DOI: 10.1021/acs.jctc.7b01232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ryan M. Richard
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - Brandon W. Bakr
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, United States
| |
Collapse
|
43
|
Cole WTS, Farrell JD, Sheikh AA, Yönder Ö, Fellers RS, Viant MR, Wales DJ, Saykally RJ. Terahertz VRT spectroscopy of the water hexamer-d12 prism: Dramatic enhancement of bifurcation tunneling upon librational excitation. J Chem Phys 2018. [DOI: 10.1063/1.5006195] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- William T. S. Cole
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - James D. Farrell
- CAS Key Laboratory of Soft Matter Physics, Beijing National Laboratory for Condensed Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, China
| | - Akber A. Sheikh
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Öezlem Yönder
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, North Rhine-Westphalia, Germany
| | - Raymond S. Fellers
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Mark R. Viant
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - David J. Wales
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Richard J. Saykally
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| |
Collapse
|
44
|
Temelso B, Klein KL, Mabey JW, Pérez C, Pate BH, Kisiel Z, Shields GC. Exploring the Rich Potential Energy Surface of (H2O)11 and Its Physical Implications. J Chem Theory Comput 2018; 14:1141-1153. [DOI: 10.1021/acs.jctc.7b00938] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Berhane Temelso
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Katurah L. Klein
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Joel W. Mabey
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| | - Cristóbal Pérez
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
- Max Planck Institute for the Structure and Dynamics of Matter, Luruper Chausse 149, D-22761 Hamburg, Germany
| | - Brooks H. Pate
- Department
of Chemistry, University of Virginia, McCormick Road, Charlottesville, Virginia 22904-4319, United States
| | - Zbigniew Kisiel
- Institute
of Physics, Polish Academy of Sciences, Al. Lotników 32/46, 02-668 Warszawa, Poland
| | - George C. Shields
- Provost’s
Office and Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
- Dean’s
Office, College of Arts and Sciences, and Department of Chemistry, Bucknell University, Lewisburg, Pennsylvania 17837, United States
| |
Collapse
|
45
|
Dohn AO, Jónsson EÖ, Levi G, Mortensen JJ, Lopez-Acevedo O, Thygesen KS, Jacobsen KW, Ulstrup J, Henriksen NE, Møller KB, Jónsson H. Grid-Based Projector Augmented Wave (GPAW) Implementation of Quantum Mechanics/Molecular Mechanics (QM/MM) Electrostatic Embedding and Application to a Solvated Diplatinum Complex. J Chem Theory Comput 2017; 13:6010-6022. [PMID: 29083921 DOI: 10.1021/acs.jctc.7b00621] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
A multiscale density functional theory-quantum mechanics/molecular mechanics (DFT-QM/MM) scheme is presented, based on an efficient electrostatic coupling between the electronic density obtained from a grid-based projector augmented wave (GPAW) implementation of density functional theory and a classical potential energy function. The scheme is implemented in a general fashion and can be used with various choices for the descriptions of the QM or MM regions. Tests on H2O clusters, ranging from dimer to decamer show that no systematic energy errors are introduced by the coupling that exceeds the differences in the QM and MM descriptions. Over 1 ns of liquid water, Born-Oppenheimer QM/MM molecular dynamics (MD) are sampled combining 10 parallel simulations, showing consistent liquid water structure over the QM/MM border. The method is applied in extensive parallel MD simulations of an aqueous solution of the diplatinum [Pt2(P2O5H2)4]4- complex (PtPOP), spanning a total time period of roughly half a nanosecond. An average Pt-Pt distance deviating only 0.01 Å from experimental results, and a ground-state Pt-Pt oscillation frequency deviating by <2% from experimental results were obtained. The simulations highlight a remarkable harmonicity of the Pt-Pt oscillation, while also showing clear signs of Pt-H hydrogen bonding and directional coordination of water molecules along the Pt-Pt axis of the complex.
Collapse
Affiliation(s)
- A O Dohn
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - E Ö Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland
| | - G Levi
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J J Mortensen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - O Lopez-Acevedo
- Department of Applied Physics, Aalto University , 02150 Espoo, Finland
| | - K S Thygesen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K W Jacobsen
- CAMD, Department of Physics, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - J Ulstrup
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - N E Henriksen
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - K B Møller
- Department of Chemistry, Technical University of Denmark , 2800 Kgs. Lyngby, Denmark
| | - H Jónsson
- Faculty of Physical Sciences and Science Institute, University of Iceland , 107 Reykjavı́k, Iceland.,Department of Applied Physics, Aalto University , 02150 Espoo, Finland
| |
Collapse
|
46
|
Holmes JD, Otero-de-la-Roza A, DiLabio GA. Accurate Modeling of Water Clusters with Density-Functional Theory Using Atom-Centered Potentials. J Chem Theory Comput 2017; 13:4205-4215. [DOI: 10.1021/acs.jctc.7b00624] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jake D. Holmes
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Gino A. DiLabio
- Department
of Chemistry and ‡Faculty of Management, The University of British Columbia, 3247
University Way, Kelowna, British Columbia, Canada V1V 1V7
| |
Collapse
|
47
|
Manna D, Kesharwani MK, Sylvetsky N, Martin JML. Conventional and Explicitly Correlated ab Initio Benchmark Study on Water Clusters: Revision of the BEGDB and WATER27 Data Sets. J Chem Theory Comput 2017; 13:3136-3152. [DOI: 10.1021/acs.jctc.6b01046] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Debashree Manna
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Manoj K. Kesharwani
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Nitai Sylvetsky
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| | - Jan M. L. Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 76100 Rechovot, Israel
| |
Collapse
|
48
|
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
| |
Collapse
|
49
|
Yuan D, Li Y, Ni Z, Pulay P, Li W, Li S. Benchmark Relative Energies for Large Water Clusters with the Generalized Energy-Based Fragmentation Method. J Chem Theory Comput 2017; 13:2696-2704. [DOI: 10.1021/acs.jctc.7b00284] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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 210023, P. R. China
| | - Yunzhi 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 210023, P. R. China
| | - Zhigang Ni
- School
of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic
Chemistry of Ministry of Education, Institute of Theoretical and Computational
Chemistry, Nanjing University, Nanjing 210023, P. R. China
| | - Peter Pulay
- Department
of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - 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 210023, P. R. China
| | - 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 210023, P. R. China
| |
Collapse
|
50
|
Brown SE, Götz AW, Cheng X, Steele RP, Mandelshtam VA, Paesani F. Monitoring Water Clusters “Melt” Through Vibrational Spectroscopy. J Am Chem Soc 2017; 139:7082-7088. [DOI: 10.1021/jacs.7b03143] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | | | - Xiaolu Cheng
- Department
of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | - Ryan P. Steele
- Department
of Chemistry and Henry Eyring Center for Theoretical Chemistry, University of Utah, Salt Lake City, Utah 84112, United States
| | | | | |
Collapse
|