1
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Bergami M, Charry J, Reyes A, Coutinho K, Varella MTDN. Does Positron Attachment Take Place in Water Solution? J Phys Chem B 2024. [PMID: 39382199 DOI: 10.1021/acs.jpcb.4c03627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2024]
Abstract
We performed a computational study of positron attachment to hydrated amino acids, namely glycine, alanine, and proline in the zwitterionic form. We combined the sequential quantum mechanics/molecular mechanics (s-QM/MM) method with various levels of any particle molecular orbital (APMO) calculations. Consistent with previous studies, our calculations indicate the formation of energetically stable states for the isolated and microsolvated amino acids, in which the positron localizes around the carboxylate group. However, for the larger clusters, composed of 7 to 40 water molecules, hydrogen bonding between the solute and solvent molecules disfavors positron attachment to the amino acids, giving rise to surface states in which the positron is located around the water-vacuum interface. The analysis of positron binding energies, positronic orbitals, radial probability distributions, and annihilation rates consistently pointed out the change from positron-solute to positron-solvent states. Even with the inclusion of an electrostatic embedding around the aggregates, the positrons did not localize around the solute. Positron attachment to molecules in the gas phase is a well-established fact. The existence of hydrated positronic molecules could also be expected from the analogy with transient anion states, which are believed to participate in radiation damage. Our results indicate that positron attachment to hydrated biomolecules, even to zwitterions with negatively charged carboxylated groups, would not take place. For the larger clusters, in which positron-water interactions are favored, the calculations indicate an unexpectedly large contribution of the core orbitals to the annihilation rates, between 15 and 20%. Finally, we explored correlations between positron binding energies (PBEs) and dipole moments, as well as annihilation rates and PBEs, consistent with previous studies for smaller clusters.
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Affiliation(s)
- Mateus Bergami
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, CEP 05508-090 São Paulo, SP, Brazil
| | - Jorge Charry
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - Andres Reyes
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra. 30 #45-03, 111321 Bogotá, Colombia
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, CEP 05508-090 São Paulo, SP, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1371, CEP 05508-090 São Paulo, SP, Brazil
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2
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Kovtun M, Lambros E, Liu A, Tang D, Williams-Young DB, Li X. Accelerating Relativistic Exact-Two-Component Density Functional Theory Calculations with Graphical Processing Units. J Chem Theory Comput 2024. [PMID: 39226542 DOI: 10.1021/acs.jctc.4c00843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Numerical integration of the exchange-correlation potential is an inherently parallel problem that can be significantly accelerated by graphical processing units (GPUs). In this Letter, we present the first implementation of GPU-accelerated exchange-correlation potential in the GauXC library for relativistic, 2-component density functional theory. By benchmarking against copper, silver, and gold coinage metal clusters, we demonstrate the speed and efficiency of our implementation, achieving significant speedup compared to CPU-based calculations. One GPU card provides computational power equivalent to roughly 400 CPU cores in the context of this work. The speedup further increases for larger systems, highlighting the potential of our approach for future, more computationally demanding simulations. Our implementation supports arbitrary angular momentum basis functions, enabling the simulation of systems with heavy elements and providing substantial speedup to relativistic electronic structure calculations. This advancement paves the way for more efficient and extensive computational studies in the field of density functional theory.
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Affiliation(s)
- Mikael Kovtun
- Department of Chemistry, University of Washington Seattle, Washington 98115, United States
| | - Eleftherios Lambros
- Department of Chemistry, University of Washington Seattle, Washington 98115, United States
| | - Aodong Liu
- Department of Chemistry, University of Washington Seattle, Washington 98115, United States
| | - Diandong Tang
- Department of Chemistry, University of Washington Seattle, Washington 98115, United States
| | - David B Williams-Young
- Applied Mathematics and Computational Research Division Lawrence Berkeley National Laboratory Berkeley, California 94720, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington Seattle, Washington 98115, United States
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3
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Williams CD, Kalayan J, Burton NA, Bryce RA. Stable and accurate atomistic simulations of flexible molecules using conformationally generalisable machine learned potentials. Chem Sci 2024; 15:12780-12795. [PMID: 39148799 PMCID: PMC11323334 DOI: 10.1039/d4sc01109k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Accepted: 07/07/2024] [Indexed: 08/17/2024] Open
Abstract
Computational simulation methods based on machine learned potentials (MLPs) promise to revolutionise shape prediction of flexible molecules in solution, but their widespread adoption has been limited by the way in which training data is generated. Here, we present an approach which allows the key conformational degrees of freedom to be properly represented in reference molecular datasets. MLPs trained on these datasets using a global descriptor scheme are generalisable in conformational space, providing quantum chemical accuracy for all conformers. These MLPs are capable of propagating long, stable molecular dynamics trajectories, an attribute that has remained a challenge. We deploy the MLPs in obtaining converged conformational free energy surfaces for flexible molecules via well-tempered metadynamics simulations; this approach provides a hitherto inaccessible route to accurately computing the structural, dynamical and thermodynamical properties of a wide variety of flexible molecular systems. It is further demonstrated that MLPs must be trained on reference datasets with complete coverage of conformational space, including in barrier regions, to achieve stable molecular dynamics trajectories.
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Affiliation(s)
- Christopher D Williams
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Jas Kalayan
- Science and Technologies Facilities Council (STFC), Daresbury Laboratory Keckwick Lane, Daresbury Warrington WA4 4AD UK
| | - Neil A Burton
- Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester Oxford Road Manchester M13 9PL UK
| | - Richard A Bryce
- Division of Pharmacy and Optometry, School of Health Sciences, Faculty of Biology, Medicine and Health, The University of Manchester Oxford Road Manchester M13 9PL UK
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4
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Slattery SA, Yon JC, Valeev EF. Revisiting Artifacts of Kohn-Sham Density Functionals for Biosimulation. J Chem Theory Comput 2024; 20:6652-6660. [PMID: 39083031 PMCID: PMC11325537 DOI: 10.1021/acs.jctc.4c00712] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/17/2024]
Abstract
We revisit the problem of unphysical charge density delocalization/fractionalization induced by the self-interaction error of common approximate Kohn-Sham (KS) density functional theory functionals on simulation of small to medium-sized proteins in a vacuum. Aside from producing unphysical electron densities and total energies, the vanishing of the HOMO-LUMO gap associated with the unphysical charge delocalization leads to an unphysical low-energy spectrum and catastrophic failure of most popular solvers for the KS self-consistent field (SCF) problem. We apply a robust quasi-Newton SCF solver [ Phys. Chem. Chem. Phys. 2024, 26, 6557] to obtain solutions for some of these difficult cases. The anatomy of the charge delocalization is revealed by the natural deformation orbitals obtained from the density matrix difference between the Hartree-Fock and KS solutions; the charge delocalization not only can occur between charged fragments (such as in zwitterionic polypeptides) but also involves neutral fragments. The vanishing-gap phenomenon and troublesome SCF convergence are both attributed to the unphysical KS Fock operator eigenspectra of molecular fragments (e.g., amino acids or their side chains). Analysis of amino acid pairs suggests that the unphysical charge delocalization can be partially ameliorated by the use of some range-separated hybrid functionals but not by semilocal or standard hybrid functionals. Last, we demonstrate that solutions without the unphysical charge delocalization can be located even for semilocal KS functionals highly prone to such defects, but such solutions have non-Aufbau character and are unstable with respect to mixing of the non-overlapping "frontier" orbitals. Caution should be exercised when unexpectedly small (or vanishing) HOMO-LUMO gaps and atypical SCF convergence patterns (e.g., oscillatory) are observed in KS DFT simulations in any context (bio or otherwise).
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Affiliation(s)
- Samuel A Slattery
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Jaden C Yon
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | - Edward F Valeev
- Department of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
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5
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Kiataki MB, Coutinho K, Varella MTDN. Toward a numerically efficient description of bulk-solvated anionic states. J Chem Phys 2024; 161:034301. [PMID: 39007383 DOI: 10.1063/5.0203247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2024] [Accepted: 06/27/2024] [Indexed: 07/16/2024] Open
Abstract
We investigate the vertical electron attachment energy (VAE) of 1-methyl-4-nitroimidazole, a model radiosensitizer, employing quantum mechanics/molecular mechanics (QM/MM) and QM/polarized continuum (QM/PCM) solvation models. We considered the solvent-excluded surface (QM/PCM-SES) and Van der Waals (QM/PCM-VDW) cavities within the PCM framework, the electrostatic embedding QM/MM (EE-QM/MM) model, and the self-consistent sequential QM/MM polarizable electrostatic embedding (scPEE-S-QM/MM) model. Due to slow VAE convergence concerning the number of QM solvent molecules, full QM calculations prove inefficient. Ensemble averages in these calculations do not align with VAEs computed for the representative solute-solvent configuration. QM/MM and QM/PCM calculations show agreement with each other for sufficiently large QM regions, although the QM/PCM-VDW model exhibits artifacts linked to the cavity. QM/MM models demonstrate good agreement between ensemble averages and VAEs calculated with the representative configuration. Notably, the VAE computed with the scPEE-S-QM/MM model achieves faster convergence concerning the number of QM water molecules compared to the EE-QM/MM model, attributed to enhanced efficiency from MM charge polarization in the scPEE-S-QM/MM approach. This emphasizes the importance of QM/classical models with accurate solute-solvent and solvent-solvent mutual polarization for obtaining converged VAEs at a reasonable computational cost. The full-QM approach is very inefficient, while the microsolvation model is inaccurate. Computational savings in QM/MM models result from electrostatic embedding and the representative configuration, with the scPEE-S-QM/MM approach emerging as an efficient tool for describing bulk-solvated anions within the QM/MM framework. Its potential extends to improving transient anion state descriptions in biomolecules and radiosensitizers, especially given the frequent employment of microsolvation models.
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Affiliation(s)
- Matheus B Kiataki
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Kaline Coutinho
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
| | - Márcio T do N Varella
- Instituto de Física, Universidade de São Paulo, Rua do Matão 1731, 05508-090 São Paulo, Brazil
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6
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Wang B, Dou S, Wang S, Wang Y, Zhang S, Lin X, Chen Y, Ji C, Dai Y, Dong L. Mechanism of thermal oxidation into volatile compounds from (E)-4-decenal: A density functional theory study. Food Chem X 2024; 21:101174. [PMID: 38362527 PMCID: PMC10867582 DOI: 10.1016/j.fochx.2024.101174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 01/31/2024] [Accepted: 02/01/2024] [Indexed: 02/17/2024] Open
Abstract
Unsaturated aliphatic aldehyde oxidation plays a significant role in the deep oxidation of fatty acids to produce volatile chemicals. Exposing the oxidation process of unsaturated aliphatic aldehydes is crucial to completely comprehend how food flavor forms. In this study, thermal desorption cryo-trapping in conjunction with gas chromatography-mass spectrometry was used to examine the volatile profile of (E)-4-decenal during heating, and 32 volatile compounds in all were detected and identified. Meanwhile, density functional theory (DFT) calculations were used, and 43 reactions were obtained in the 24 pathways, which were summarized into the peroxide reaction mechanism (ROOH), the peroxyl radical reaction mechanism (ROO·) and the alkoxy radical reaction mechanism (RO·). Moreover, the priority of these three oxidative mechanisms was the RO· mechanism > ROOH mechanism > ROO· mechanism. Furthermore, the DFT results and experimental results agreed well, and the oxidative mechanism of (E)-4-decenal was finally illuminated.
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Affiliation(s)
- Binchen Wang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Shaohua Dou
- College of Life and Health, Dalian University, Dalian 116622, Liaoning, China
| | - Shang Wang
- School of Biotechnology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Yi Wang
- School of Biotechnology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
| | - Sufang Zhang
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Xinping Lin
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Yingxi Chen
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Chaofan Ji
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Yiwei Dai
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
| | - Liang Dong
- School of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, Liaoning, China
- National Engineering Research Centre of Seafood, Dalian 116034, Liaoning, China
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7
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Mamatkulov K, Zavatski S, Arynbek Y, Esawii HA, Burko A, Bandarenka H, Arzumanyan G. Conformational analysis of lipid membrane mimetics modified with A β42 peptide by Raman spectroscopy and computer simulations. J Biomol Struct Dyn 2024:1-14. [PMID: 38520152 DOI: 10.1080/07391102.2024.2330706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/08/2024] [Indexed: 03/25/2024]
Abstract
Peptide-lipid interactions play an important role in maintaining the integrity and function of the cell membrane. Even slight changes in these interactions can induce the development of various diseases. Specifically, peptide misfolding and aggregation in the membrane is considered to be one of the triggers of Alzheimer's disease (AD), however its exact mechanism is still unclear. To this end, an increase of amyloid-beta (Aβ) peptide concentration in the human brain is widely accepted to gradually produce cytotoxic Aβ aggregates (plaques). These plaques initiate a sequence of pathogenic events ending up in observable symptoms of dementia. Understanding the mechanism of the Aβ interaction with cells is crucial for early detection and prevention of Alzheimer's disease. Hence, in this work, a comprehensive Raman analysis of the Aβ42 conformational dynamics in water and in liposomes and lipodiscs that mimic the membrane system is presented. The obtained results show that the secondary structure of Aβ42 in liposomes is dominated by the α-helix conformation, which remains stable over time. However, it comes as a surprise to reveal that the lipodisc environment induces the transformation of the Aβ42 secondary structure to a β-turn/random coil. Our Raman spectroscopy findings are supported with molecular dynamics (MD) and density functional theory (DFT) simulations, showing their good agreement.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Kahramon Mamatkulov
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
| | - Siarhei Zavatski
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Yersultan Arynbek
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Faculty of Physics and Technology, al-Farabi, Kazakh National University, Almaty, Kazakhstan
| | - Heba A Esawii
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
- Biophysics Department, Faculty of Science, Cairo University, Egypt
| | - Aliaksandr Burko
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Hanna Bandarenka
- Applied Plasmonics Laboratory, Belarusian State University of Informatics and Radioelectronics, Minsk, Belarus
| | - Grigory Arzumanyan
- Laboratory of Neutron Physics, Sector of Raman Spectroscopy, Joint Institute for Nuclear Research, Dubna, Russia
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8
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Lee AJ, Rackers JA, Pathak S, Bricker WP. Building an ab initio solvated DNA model using Euclidean neural networks. PLoS One 2024; 19:e0297502. [PMID: 38358990 PMCID: PMC10868815 DOI: 10.1371/journal.pone.0297502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2023] [Accepted: 01/06/2024] [Indexed: 02/17/2024] Open
Abstract
Accurately modeling large biomolecules such as DNA from first principles is fundamentally challenging due to the steep computational scaling of ab initio quantum chemistry methods. This limitation becomes even more prominent when modeling biomolecules in solution due to the need to include large numbers of solvent molecules. We present a machine-learned electron density model based on a Euclidean neural network framework that includes a built-in understanding of equivariance to model explicitly solvated double-stranded DNA. By training the machine learning model using molecular fragments that sample the key DNA and solvent interactions, we show that the model predicts electron densities of arbitrary systems of solvated DNA accurately, resolves polarization effects that are neglected by classical force fields, and captures the physics of the DNA-solvent interaction at the ab initio level.
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Affiliation(s)
- Alex J. Lee
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, United States of America
| | - Joshua A. Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America
| | - Shivesh Pathak
- Center for Computing Research, Sandia National Laboratories, Albuquerque, NM, United States of America
| | - William P. Bricker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, NM, United States of America
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9
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Villot C, Huang T, Lao KU. Accurate prediction of global-density-dependent range-separation parameters based on machine learning. J Chem Phys 2023; 159:044103. [PMID: 37486048 DOI: 10.1063/5.0157340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2023] [Accepted: 07/03/2023] [Indexed: 07/25/2023] Open
Abstract
In this work, we develop an accurate and efficient XGBoost machine learning model for predicting the global-density-dependent range-separation parameter, ωGDD, for long-range corrected functional (LRC)-ωPBE. This ωGDDML model has been built using a wide range of systems (11 466 complexes, ten different elements, and up to 139 heavy atoms) with fingerprints for the local atomic environment and histograms of distances for the long-range atomic correlation for mapping the quantum mechanical range-separation values. The promising performance on the testing set with 7046 complexes shows a mean absolute error of 0.001 117 a0-1 and only five systems (0.07%) with an absolute error larger than 0.01 a0-1, which indicates the good transferability of our ωGDDML model. In addition, the only required input to obtain ωGDDML is the Cartesian coordinates without electronic structure calculations, thereby enabling rapid predictions. LRC-ωPBE(ωGDDML) is used to predict polarizabilities for a series of oligomers, where polarizabilities are sensitive to the asymptotic density decay and are crucial in a variety of applications, including the calculations of dispersion corrections and refractive index, and surpasses the performance of all other popular density functionals except for the non-tuned LRC-ωPBE. Finally, LRC-ωPBE (ωGDDML) combined with (extended) symmetry-adapted perturbation theory is used in calculating noncovalent interactions to further show that the traditional ab initio system-specific tuning procedure can be bypassed. The present study not only provides an accurate and efficient way to determine the range-separation parameter for LRC-ωPBE but also shows the synergistic benefits of fusing the power of physically inspired density functional LRC-ωPBE and the data-driven ωGDDML model.
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Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Tong Huang
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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10
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Woo J, Kim S, Kim WY. Gaussian-Approximated Poisson Preconditioner for Iterative Diagonalization in Real-Space Density Functional Theory. J Phys Chem A 2023; 127:3883-3893. [PMID: 37094552 DOI: 10.1021/acs.jpca.2c09111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Various real-space methods optimized on massive parallel computers have been developed for efficient large-scale density functional theory (DFT) calculations of materials and biomolecules. The iterative diagonalization of the Hamiltonian matrix is a computational bottleneck in real-space DFT calculations. Despite the development of various iterative eigensolvers, the absence of efficient real-space preconditioners has hindered their overall efficiency. An efficient preconditioner must satisfy two conditions: appropriate acceleration of the convergence of the iterative process and inexpensive computation. This study proposed a Gaussian-approximated Poisson preconditioner (GAPP) that satisfied both conditions and was suitable for real-space methods. A low computational cost was realized through the Gaussian approximation of a Poisson Green's function. Fast convergence was achieved through the proper determination of Gaussian coefficients to fit the Coulomb energies. The performance of GAPP was evaluated for several molecular and extended systems, and it showed the highest efficiency among the existing preconditioners adopted in real-space codes.
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Affiliation(s)
- Jeheon Woo
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Seonghwan Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Woo Youn Kim
- Department of Chemistry, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
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11
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Raghavan B, Schackert FK, Levy A, Johnson SK, Ippoliti E, Mandelli D, Olsen JMH, Rothlisberger U, Carloni P. MiMiCPy: An Efficient Toolkit for MiMiC-Based QM/MM Simulations. J Chem Inf Model 2023; 63:1406-1412. [PMID: 36811959 PMCID: PMC10015468 DOI: 10.1021/acs.jcim.2c01620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
MiMiC is a highly flexible, extremely scalable multiscale modeling framework. It couples the CPMD (quantum mechanics, QM) and GROMACS (molecular mechanics, MM) codes. The code requires preparing separate input files for the two programs with a selection of the QM region. This can be a tedious procedure prone to human error, especially when dealing with large QM regions. Here, we present MiMiCPy, a user-friendly tool that automatizes the preparation of MiMiC input files. It is written in Python 3 with an object-oriented approach. The main subcommand PrepQM can be used to generate MiMiC inputs directly from the command line or through a PyMOL/VMD plugin for visually selecting the QM region. Many other subcommands are also provided for debugging and fixing MiMiC input files. MiMiCPy is designed with a modular structure that allows seamless extensions to new program formats depending on the requirements of MiMiC.
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Affiliation(s)
- Bharath Raghavan
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany.,Department of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - Florian K Schackert
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany.,Department of Physics, RWTH Aachen University, Aachen 52074, Germany
| | - Andrea Levy
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Sophia K Johnson
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Emiliano Ippoliti
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | - Davide Mandelli
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany
| | | | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry, Institute of Chemical Sciences and Engineering, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Paolo Carloni
- Computational Biomedicine, Institute of Advanced Simulations IAS-5/Institute for Neuroscience and Medicine INM-9, Forschungszentrum Jülich GmbH, Jülich 52428, Germany.,Department of Physics, RWTH Aachen University, Aachen 52074, Germany
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12
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Chandy SK, Raghavachari K. Accurate and Cost-Effective NMR Chemical Shift Predictions for Nucleic Acids Using a Molecules-in-Molecules Fragmentation-Based Method. J Chem Theory Comput 2023; 19:544-561. [PMID: 36630261 DOI: 10.1021/acs.jctc.2c00967] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
We have developed, implemented, and assessed an efficient protocol for the prediction of NMR chemical shifts of large nucleic acids using our molecules-in-molecules (MIM) fragment-based quantum chemical approach. To assess the performance of our approach, MIM-NMR calculations are calibrated on a test set of three nucleic acids, where the structure is derived from solution-phase NMR studies. For DNA systems with multiple conformers, the one-layer MIM method with trimer fragments (MIM1trimer) is benchmarked to get the lowest energy structure, with an average error of only 0.80 kcal/mol with respect to unfragmented full molecule calculations. The MIMI-NMRdimer calibration with respect to unfragmented full molecule calculations shows a mean absolute deviation (MAD) of 0.06 and 0.11 ppm, respectively, for 1H and 13C nuclei, but the performance with respect to experimental NMR chemical shifts is comparable to the more expensive MIM1-NMR and MIM2-NMR methods with trimer subsystems. To compare with the experimental chemical shifts, a standard protocol is derived using DNA systems with Protein Data Bank (PDB) IDs 1SY8, 1K2K, and 1KR8. The effect of structural minimizations is employed using a hybrid mechanics/semiempirical approach and used for computations in solution with implicit and explicit-implicit solvation models in our MIM1-NMRdimer methodology. To demonstrate the applicability of our protocol, we tested it on seven nucleic acids, including structures with nonstandard residues, heteroatom substitutions (F and B atoms), and side chain mutations with a size ranging from ∼300 to 1100 atoms. The major improvement for predicted MIM1-NMRdimer calculations is obtained from structural minimizations and implicit solvation effects. A significant improvement with the explicit-implicit solvation model is observed only for two smaller nucleic acid systems (1KR8 and 7NBK), where the expensive first solvation shell is replaced by the microsolvation model, in which a single water molecule is added for each solvent-exposed amino and imino protons, along with the implicit solvation. Overall, our target accuracy of ∼0.2-0.3 ppm for 1H and ∼2-3 ppm for 13C has been achieved for large nucleic acids. The proposed MIM-NMR approach is accurate and cost-effective (linear scaling with system size), and it can aid in the structural assignments of a wide range of complex biomolecules.
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Affiliation(s)
- Sruthy K Chandy
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
| | - Krishnan Raghavachari
- Department of Chemistry, Indiana University, Bloomington, Indiana 47405, United States
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13
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Lee AJ, Rackers JA, Bricker WP. Predicting accurate ab initio DNA electron densities with equivariant neural networks. Biophys J 2022; 121:3883-3895. [PMID: 36057785 PMCID: PMC9674991 DOI: 10.1016/j.bpj.2022.08.045] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 07/22/2022] [Accepted: 08/29/2022] [Indexed: 11/19/2022] Open
Abstract
One of the fundamental limitations of accurately modeling biomolecules like DNA is the inability to perform quantum chemistry calculations on large molecular structures. We present a machine learning model based on an equivariant Euclidean neural network framework to obtain accurate ab initio electron densities for arbitrary DNA structures that are much too large for conventional quantum methods. The model is trained on representative B-DNA basepair steps that capture both base pairing and base stacking interactions. The model produces accurate electron densities for arbitrary B-DNA structures with typical errors of less than 1%. Crucially, the error does not increase with system size, which suggests that the model can extrapolate to large DNA structures with negligible loss of accuracy. The model also generalizes reasonably to other DNA structural motifs such as the A- and Z-DNA forms, despite being trained on only B-DNA configurations. The model is used to calculate electron densities of several large-scale DNA structures, and we show that the computational scaling for this model is essentially linear. We also show that this machine learning electron density model can be used to calculate accurate electrostatic potentials for DNA. These electrostatic potentials produce more accurate results compared with classical force fields and do not show the usual deficiencies at short range.
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Affiliation(s)
- Alex J Lee
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico
| | - Joshua A Rackers
- Center for Computing Research, Sandia National Laboratories, Albuquerque, New Mexico.
| | - William P Bricker
- Department of Chemical and Biological Engineering, University of New Mexico, Albuquerque, New Mexico.
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14
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Amin SA, Kumar J, Khatun S, Das S, Qureshi IA, Jha T, Gayen S. Binary quantitative activity-activity relationship (QAAR) studies to explore selective HDAC8 inhibitors: In light of mathematical models, DFT-based calculation and molecular dynamic simulation studies. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132833] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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15
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Prentice JCA. Efficiently Computing Excitations of Complex Systems: Linear-Scaling Time-Dependent Embedded Mean-Field Theory in Implicit Solvent. J Chem Theory Comput 2022; 18:1542-1554. [PMID: 35133827 PMCID: PMC9082505 DOI: 10.1021/acs.jctc.1c01133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Quantum embedding schemes have the
potential to significantly reduce
the computational cost of first-principles calculations while maintaining
accuracy, particularly for calculations of electronic excitations
in complex systems. In this work, I combine time-dependent embedded
mean field theory (TD-EMFT) with linear-scaling density functional
theory and implicit solvation models, extending previous work within
the ONETEP code. This provides a way to perform multilevel calculations
of electronic excitations on very large systems, where long-range
environmental effects, both quantum and classical in nature, are important.
I demonstrate the power of this method by performing simulations on
a variety of systems, including a molecular dimer, a chromophore in
solution, and a doped molecular crystal. This work paves the way for
high accuracy calculations to be performed on large-scale systems
that were previously beyond the reach of quantum embedding schemes.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, United Kingdom
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16
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Gray M, Herbert JM. Simplified tuning of long-range corrected density functionals for use in symmetry-adapted perturbation theory. J Chem Phys 2021; 155:034103. [PMID: 34293871 DOI: 10.1063/5.0059364] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Long considered a failure, second-order symmetry-adapted perturbation theory (SAPT) based on Kohn-Sham orbitals, or SAPT0(KS), can be resurrected for semiquantitative purposes using long-range corrected density functionals whose asymptotic behavior is adjusted separately for each monomer. As in other contexts, correct asymptotic behavior can be enforced via "optimal tuning" based on the ionization energy theorem of density functional theory, but the tuning procedure is tedious, expensive for large systems, and comes with a troubling dependence on system size. Here, we show that essentially identical results are obtained using a fast, convenient, and automated tuning procedure based on the size of the exchange hole. In conjunction with "extended" (X)SAPT methods that improve the description of dispersion, this procedure achieves benchmark-quality interaction energies, along with the usual SAPT energy decomposition, without the hassle of system-specific tuning.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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17
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Chen M, Baer R, Neuhauser D, Rabani E. Stochastic density functional theory: Real- and energy-space fragmentation for noise reduction. J Chem Phys 2021; 154:204108. [PMID: 34241170 DOI: 10.1063/5.0044163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Stochastic density functional theory (sDFT) is becoming a valuable tool for studying ground-state properties of extended materials. The computational complexity of describing the Kohn-Sham orbitals is replaced by introducing a set of random (stochastic) orbitals leading to linear and often sub-linear scaling of certain ground-state observables at the account of introducing a statistical error. Schemes to reduce the noise are essential, for example, for determining the structure using the forces obtained from sDFT. Recently, we have introduced two embedding schemes to mitigate the statistical fluctuations in the electron density and resultant forces on the nuclei. Both techniques were based on fragmenting the system either in real space or slicing the occupied space into energy windows, allowing for a significant reduction in the statistical fluctuations. For chemical accuracy, further reduction of the noise is required, which could be achieved by increasing the number of stochastic orbitals. However, the convergence is relatively slow as the statistical error scales as 1/Nχ according to the central limit theorem, where Nχ is the number of random orbitals. In this paper, we combined the embedding schemes mentioned above and introduced a new approach that builds on overlapped fragments and energy windows. The new approach significantly lowers the noise for ground-state properties, such as the electron density, total energy, and forces on the nuclei, as demonstrated for a G-center in bulk silicon.
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Affiliation(s)
- Ming Chen
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Roi Baer
- Fritz Haber Center of Molecular Dynamics and Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Daniel Neuhauser
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California 90095, USA
| | - Eran Rabani
- Department of Chemistry, University of California, Berkeley, California 94720, USA
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18
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Analysis of Photosynthetic Systems and Their Applications with Mathematical and Computational Models. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10196821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
In biological and life science applications, photosynthesis is an important process that involves the absorption and transformation of sunlight into chemical energy. During the photosynthesis process, the light photons are captured by the green chlorophyll pigments in their photosynthetic antennae and further funneled to the reaction center. One of the most important light harvesting complexes that are highly important in the study of photosynthesis is the membrane-attached Fenna–Matthews–Olson (FMO) complex found in the green sulfur bacteria. In this review, we discuss the mathematical formulations and computational modeling of some of the light harvesting complexes including FMO. The most recent research developments in the photosynthetic light harvesting complexes are thoroughly discussed. The theoretical background related to the spectral density, quantum coherence and density functional theory has been elaborated. Furthermore, details about the transfer and excitation of energy in different sites of the FMO complex along with other vital photosynthetic light harvesting complexes have also been provided. Finally, we conclude this review by providing the current and potential applications in environmental science, energy, health and medicine, where such mathematical and computational studies of the photosynthesis and the light harvesting complexes can be readily integrated.
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19
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Lynch C, Rao S, Sansom MSP. Water in Nanopores and Biological Channels: A Molecular Simulation Perspective. Chem Rev 2020; 120:10298-10335. [PMID: 32841020 PMCID: PMC7517714 DOI: 10.1021/acs.chemrev.9b00830] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Indexed: 12/18/2022]
Abstract
This Review explores the dynamic behavior of water within nanopores and biological channels in lipid bilayer membranes. We focus on molecular simulation studies, alongside selected structural and other experimental investigations. Structures of biological nanopores and channels are reviewed, emphasizing those high-resolution crystal structures, which reveal water molecules within the transmembrane pores, which can be used to aid the interpretation of simulation studies. Different levels of molecular simulations of water within nanopores are described, with a focus on molecular dynamics (MD). In particular, models of water for MD simulations are discussed in detail to provide an evaluation of their use in simulations of water in nanopores. Simulation studies of the behavior of water in idealized models of nanopores have revealed aspects of the organization and dynamics of nanoconfined water, including wetting/dewetting in narrow hydrophobic nanopores. A survey of simulation studies in a range of nonbiological nanopores is presented, including carbon nanotubes, synthetic nanopores, model peptide nanopores, track-etched nanopores in polymer membranes, and hydroxylated and functionalized nanoporous silica. These reveal a complex relationship between pore size/geometry, the nature of the pore lining, and rates of water transport. Wider nanopores with hydrophobic linings favor water flow whereas narrower hydrophobic pores may show dewetting. Simulation studies over the past decade of the behavior of water in a range of biological nanopores are described, including porins and β-barrel protein nanopores, aquaporins and related polar solute pores, and a number of different classes of ion channels. Water is shown to play a key role in proton transport in biological channels and in hydrophobic gating of ion channels. An overall picture emerges, whereby the behavior of water in a nanopore may be predicted as a function of its hydrophobicity and radius. This informs our understanding of the functions of diverse channel structures and will aid the design of novel nanopores. Thus, our current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa. However, to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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Affiliation(s)
- Charlotte
I. Lynch
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Shanlin Rao
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
| | - Mark S. P. Sansom
- Department of Biochemistry, University of Oxford, South Parks Road, Oxford, OX1 3QU, U.K.
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20
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Linscott EB, Cole DJ, Hine NDM, Payne MC, Weber C. ONETEP + TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory. J Chem Theory Comput 2020; 16:4899-4911. [PMID: 32433876 DOI: 10.1021/acs.jctc.0c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlated electronic behavior while simultaneously including the effects of the environment, making it ideally suited for studying complex and heterogeneous systems that contain transition metals and lanthanides, such as metalloproteins. We systematically introduce the necessary formalism, which must account for the nonorthogonal basis set used by ONETEP. In order to demonstrate the capabilities of this code, we apply it to carbon monoxide ligated iron porphyrin and explore the distinctly quantum-mechanical character of the iron 3d electrons during the process of photodissociation.
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Affiliation(s)
- Edward B Linscott
- Theory and Simulation of Materials (THEOS), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Michael C Payne
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Cédric Weber
- Theory and Simulation of Condensed Matter, King's College London, The Strand, London WC2R 2LS, United Kingdom
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21
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García A, Papior N, Akhtar A, Artacho E, Blum V, Bosoni E, Brandimarte P, Brandbyge M, Cerdá JI, Corsetti F, Cuadrado R, Dikan V, Ferrer J, Gale J, García-Fernández P, García-Suárez VM, García S, Huhs G, Illera S, Korytár R, Koval P, Lebedeva I, Lin L, López-Tarifa P, Mayo SG, Mohr S, Ordejón P, Postnikov A, Pouillon Y, Pruneda M, Robles R, Sánchez-Portal D, Soler JM, Ullah R, Yu VWZ, Junquera J. Siesta: Recent developments and applications. J Chem Phys 2020; 152:204108. [DOI: 10.1063/5.0005077] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Affiliation(s)
- Alberto García
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | - Nick Papior
- DTU Computing Center, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Arsalan Akhtar
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Emilio Artacho
- CIC Nanogune BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain
- Ikerbasque, Basque Foundation for Science, 48011 Bilbao, Spain
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, United Kingdom
| | - Volker Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
- Department of Chemistry, Duke University, Durham, North Carolina 27708, USA
| | - Emanuele Bosoni
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | - Pedro Brandimarte
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain
| | - Mads Brandbyge
- DTU Physics, Center for Nanostructured Graphene (CNG), Technical University of Denmark, Kgs. Lyngby DK-2800, Denmark
| | - J. I. Cerdá
- Instituto de Ciencia de Materiales de Madrid ICMM-CSIC, Cantoblanco, 28049 Madrid, Spain
| | - Fabiano Corsetti
- CIC Nanogune BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
| | - Ramón Cuadrado
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Vladimir Dikan
- Institut de Ciència de Materials de Barcelona (ICMAB-CSIC), Bellaterra E-08193, Spain
| | - Jaime Ferrer
- Department of Physics, University of Oviedo, Oviedo 33007, Spain
- Nanomaterials and Nanotechnology Research Center, CSIC - Universidad de Oviedo, Oviedo 33007, Spain
| | - Julian Gale
- Curtin Institute for Computation, Institute for Geoscience Research (TIGeR), School of Molecular and Life Sciences, Curtin University, P.O. Box U1987, Perth, WA 6845, Australia
| | - Pablo García-Fernández
- Departamento de Ciencias de la Tierra y Física de la Materia Condensada, Universidad de Cantabria, Cantabria Campus Internacional, Avenida de los Castros s/n, 39005 Santander, Spain
| | - V. M. García-Suárez
- Department of Physics, University of Oviedo, Oviedo 33007, Spain
- Nanomaterials and Nanotechnology Research Center, CSIC - Universidad de Oviedo, Oviedo 33007, Spain
| | - Sandra García
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Georg Huhs
- Barcelona Supercomputing Center, c/Jordi Girona, 29, 08034 Barcelona, Spain
| | - Sergio Illera
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Richard Korytár
- Department of Condensed Matter Physics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 5, 121 16 Praha 2, Czech Republic
| | - Peter Koval
- Simune Atomistics S.L., Tolosa Hiribidea, 76, 20018 Donostia-San Sebastian, Spain
| | - Irina Lebedeva
- CIC Nanogune BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
| | - Lin Lin
- Department of Mathematics, University of California, Berkeley, California 94720, USA
- Computational Research Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Pablo López-Tarifa
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastian, Spain
| | - Sara G. Mayo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Stephan Mohr
- Barcelona Supercomputing Center, c/Jordi Girona, 29, 08034 Barcelona, Spain
| | - Pablo Ordejón
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Andrei Postnikov
- LCP-A2MC, Université de Lorraine, 1 Bd Arago, F-57078 Metz, France
| | - Yann Pouillon
- Departamento de Ciencias de la Tierra y Física de la Materia Condensada, Universidad de Cantabria, Cantabria Campus Internacional, Avenida de los Castros s/n, 39005 Santander, Spain
| | - Miguel Pruneda
- Catalan Institute of Nanoscience and Nanotechnology - ICN2, CSIC and BIST, Campus UAB, 08193 Bellaterra, Spain
| | - Roberto Robles
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastian, Spain
| | - Daniel Sánchez-Portal
- Donostia International Physics Center (DIPC), Paseo Manuel de Lardizabal 4, 20018 Donostia-San Sebastian, Spain
- Centro de Física de Materiales, Centro Mixto CSIC-UPV/EHU, Paseo Manuel de Lardizabal 5, 20018 Donostia-San Sebastian, Spain
| | - Jose M. Soler
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
- Instituto de Física de la Materia Condensada (IFIMAC), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Rafi Ullah
- CIC Nanogune BRTA, Tolosa Hiribidea 76, 20018 San Sebastián, Spain
- Departamento de Física de Materiales, UPV/EHU, Paseo Manuel de Lardizabal 3, 20018 Donostia-San Sebastián, Spain
| | - Victor Wen-zhe Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Javier Junquera
- Departamento de Ciencias de la Tierra y Física de la Materia Condensada, Universidad de Cantabria, Cantabria Campus Internacional, Avenida de los Castros s/n, 39005 Santander, Spain
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22
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Prentice JCA, Aarons J, Womack JC, Allen AEA, Andrinopoulos L, Anton L, Bell RA, Bhandari A, Bramley GA, Charlton RJ, Clements RJ, Cole DJ, Constantinescu G, Corsetti F, Dubois SMM, Duff KKB, Escartín JM, Greco A, Hill Q, Lee LP, Linscott E, O'Regan DD, Phipps MJS, Ratcliff LE, Serrano ÁR, Tait EW, Teobaldi G, Vitale V, Yeung N, Zuehlsdorff TJ, Dziedzic J, Haynes PD, Hine NDM, Mostofi AA, Payne MC, Skylaris CK. The ONETEP linear-scaling density functional theory program. J Chem Phys 2020; 152:174111. [PMID: 32384832 DOI: 10.1063/5.0004445] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
We present an overview of the onetep program for linear-scaling density functional theory (DFT) calculations with large basis set (plane-wave) accuracy on parallel computers. The DFT energy is computed from the density matrix, which is constructed from spatially localized orbitals we call Non-orthogonal Generalized Wannier Functions (NGWFs), expressed in terms of periodic sinc (psinc) functions. During the calculation, both the density matrix and the NGWFs are optimized with localization constraints. By taking advantage of localization, onetep is able to perform calculations including thousands of atoms with computational effort, which scales linearly with the number or atoms. The code has a large and diverse range of capabilities, explored in this paper, including different boundary conditions, various exchange-correlation functionals (with and without exact exchange), finite electronic temperature methods for metallic systems, methods for strongly correlated systems, molecular dynamics, vibrational calculations, time-dependent DFT, electronic transport, core loss spectroscopy, implicit solvation, quantum mechanical (QM)/molecular mechanical and QM-in-QM embedding, density of states calculations, distributed multipole analysis, and methods for partitioning charges and interactions between fragments. Calculations with onetep provide unique insights into large and complex systems that require an accurate atomic-level description, ranging from biomolecular to chemical, to materials, and to physical problems, as we show with a small selection of illustrative examples. onetep has always aimed to be at the cutting edge of method and software developments, and it serves as a platform for developing new methods of electronic structure simulation. We therefore conclude by describing some of the challenges and directions for its future developments and applications.
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Affiliation(s)
- Joseph C A Prentice
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Jolyon Aarons
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - James C Womack
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Alice E A Allen
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Lampros Andrinopoulos
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Lucian Anton
- UKAEA, Culham Science Centre, Abingdon OX14 3DB, United Kingdom
| | - Robert A Bell
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Arihant Bhandari
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Gabriel A Bramley
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Robert J Charlton
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Rebecca J Clements
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Gabriel Constantinescu
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Fabiano Corsetti
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Simon M-M Dubois
- Institute of Condensed Matter and Nanosciences, Université Catholique de Louvain, Louvain-la-Neuve, Belgium
| | - Kevin K B Duff
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - José María Escartín
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Andrea Greco
- Department of Physics, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Quintin Hill
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Louis P Lee
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Edward Linscott
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - David D O'Regan
- School of Physics, AMBER, and CRANN Institute, Trinity College Dublin, The University of Dublin, Dublin 2, Ireland
| | - Maximillian J S Phipps
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Álvaro Ruiz Serrano
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Edward W Tait
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Gilberto Teobaldi
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Valerio Vitale
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nelson Yeung
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Tim J Zuehlsdorff
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, USA
| | - Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
| | - Peter D Haynes
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - Arash A Mostofi
- Department of Materials, Imperial College London, Exhibition Road, London SW7 2AZ, United Kingdom
| | - Mike C Payne
- TCM Group, Cavendish Laboratory, University of Cambridge, J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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23
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Nakata A, Baker JS, Mujahed SY, Poulton JTL, Arapan S, Lin J, Raza Z, Yadav S, Truflandier L, Miyazaki T, Bowler DR. Large scale and linear scaling DFT with the CONQUEST code. J Chem Phys 2020; 152:164112. [DOI: 10.1063/5.0005074] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
- Ayako Nakata
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Jack S. Baker
- London Centre for Nanotechnology, University College London, 17-19 Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics & Astronomy, University College London, Gower St., London WC1E 6BT, United Kingdom
| | - Shereif Y. Mujahed
- London Centre for Nanotechnology, University College London, 17-19 Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics & Astronomy, University College London, Gower St., London WC1E 6BT, United Kingdom
| | - Jack T. L. Poulton
- London Centre for Nanotechnology, University College London, 17-19 Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics & Astronomy, University College London, Gower St., London WC1E 6BT, United Kingdom
| | - Sergiu Arapan
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Jianbo Lin
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Zamaan Raza
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Sushma Yadav
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - Lionel Truflandier
- Institut des Sciences Moléculaires, Université Bordeaux, 351 Cours de la Libération, 33405 Talence, France
| | - Tsuyoshi Miyazaki
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
| | - David R. Bowler
- International Centre for Materials Nanoarchitectonics (MANA), National Institute for Materials Science (NIMS), 1-1 Namiki, Tsukuba, Ibaraki 305-0044, Japan
- London Centre for Nanotechnology, University College London, 17-19 Gordon St., London WC1H 0AH, United Kingdom
- Department of Physics & Astronomy, University College London, Gower St., London WC1E 6BT, United Kingdom
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24
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Dawson W, Mohr S, Ratcliff LE, Nakajima T, Genovese L. Complexity Reduction in Density Functional Theory Calculations of Large Systems: System Partitioning and Fragment Embedding. J Chem Theory Comput 2020; 16:2952-2964. [PMID: 32216343 DOI: 10.1021/acs.jctc.9b01152] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With the development of low order scaling methods for performing Kohn-Sham density functional theory, it is now possible to perform fully quantum mechanical calculations of systems containing tens of thousands of atoms. However, with an increase in the size of the system treated comes an increase in complexity, making it challenging to analyze such large systems and determine the cause of emergent properties. To address this issue, in this paper, we present a systematic complexity reduction methodology which can break down large systems into their constituent fragments and quantify interfragment interactions. The methodology proposed here requires no a priori information or user interaction, allowing a single workflow to be automatically applied to any system of interest. We apply this approach to a variety of different systems and show how it allows for the derivation of new system descriptors, the design of QM/MM partitioning schemes, and the novel application of graph metrics to molecules and materials.
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Affiliation(s)
- William Dawson
- RIKEN Center for Computational Science, Kobe 650-0047, Japan
| | - Stephan Mohr
- Barcelona Supercomputing Center (BSC), 08034 Barcelona, Spain
| | - Laura E Ratcliff
- Department of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | | | - Luigi Genovese
- Université Grenoble Alpes, INAC-MEM, L_Sim, Grenoble F-38000, France.,CEA, INAC-MEM, L_Sim, Grenoble F-38000, France
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25
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Zaccaria M, Dawson W, Cristiglio V, Reverberi M, Ratcliff LE, Nakajima T, Genovese L, Momeni B. Designing a bioremediator: mechanistic models guide cellular and molecular specialization. Curr Opin Biotechnol 2020; 62:98-105. [DOI: 10.1016/j.copbio.2019.09.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 08/22/2019] [Accepted: 09/06/2019] [Indexed: 12/26/2022]
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26
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Liu JQ, Luo ZD, Pan Y, Kumar Singh A, Trivedi M, Kumar A. Recent developments in luminescent coordination polymers: Designing strategies, sensing application and theoretical evidences. Coord Chem Rev 2020. [DOI: 10.1016/j.ccr.2019.213145] [Citation(s) in RCA: 263] [Impact Index Per Article: 65.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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27
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Otero-de-la-Roza A, Johnson ER. Analysis of Density-Functional Errors for Noncovalent Interactions between Charged Molecules. J Phys Chem A 2019; 124:353-361. [DOI: 10.1021/acs.jpca.9b10257] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- A. Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, Nova Scotia B3H 4R2, Canada
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28
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Prentice JCA, Charlton RJ, Mostofi AA, Haynes PD. Combining Embedded Mean-Field Theory with Linear-Scaling Density-Functional Theory. J Chem Theory Comput 2019; 16:354-365. [DOI: 10.1021/acs.jctc.9b00956] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Joseph C. A. Prentice
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Robert J. Charlton
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Arash A. Mostofi
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
| | - Peter D. Haynes
- Department of Materials, Department of Physics, and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London SW7 2AZ, United Kingdom
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29
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Summers TJ, Daniel BP, Cheng Q, DeYonker NJ. Quantifying Inter-Residue Contacts through Interaction Energies. J Chem Inf Model 2019; 59:5034-5044. [DOI: 10.1021/acs.jcim.9b00804] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Thomas J. Summers
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Baty P. Daniel
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Qianyi Cheng
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
| | - Nathan J. DeYonker
- The Department of Chemistry, The University of Memphis, 213 Smith Chemistry Building, Memphis, Tennessee 38152-3550, United States
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30
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Koval P, Ljungberg MP, Müller M, Sánchez-Portal D. Toward Efficient GW Calculations Using Numerical Atomic Orbitals: Benchmarking and Application to Molecular Dynamics Simulations. J Chem Theory Comput 2019; 15:4564-4580. [PMID: 31318555 DOI: 10.1021/acs.jctc.9b00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The use of atomic orbitals in Hedin's GW approximation provides, in principle, an inexpensive alternative to plane-wave basis sets, especially when modeling large molecules. However, benchmarking of the algorithms and basis sets is essential for a careful balance between cost and accuracy. In this paper, we present an implementation of the GW approximation using numerical atomic orbitals and a pseudopotential treatment of core electrons. The combination of a contour deformation technique with a one-shot extraction of quasiparticle energies provides an efficient scheme for many applications. The performance of the implementation with respect to the basis set convergence and the effect of the use of pseudopotentials has been tested for the 117 closed-shell molecules from the G2/97 test set and 24 larger acceptor molecules from another recently proposed test set. Moreover, to demonstrate the potential of our method, we compute the thermally averaged GW density of states of a large photochromic compound by sampling ab initio molecular dynamics trajectories at different temperatures. The computed thermal line widths indicate approximately twice as large electron-phonon couplings with GW than with standard DFT-GGA calculations. This is further confirmed using frozen-phonon calculations.
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Affiliation(s)
- Peter Koval
- Donostia International Physics Center , Paseo Manuel de Lardizabal 4 , 20018 Donostia-San Sebastián , Spain
| | - Mathias Per Ljungberg
- Donostia International Physics Center , Paseo Manuel de Lardizabal 4 , 20018 Donostia-San Sebastián , Spain
| | - Moritz Müller
- Donostia International Physics Center , Paseo Manuel de Lardizabal 4 , 20018 Donostia-San Sebastián , Spain
| | - Daniel Sánchez-Portal
- Donostia International Physics Center , Paseo Manuel de Lardizabal 4 , 20018 Donostia-San Sebastián , Spain.,Centro de Física de Materiales , Centro Mixto CSIC-UPV/EHU , Paseo Manuel de Lardizabal 5 , 20018 Donostia-San Sebastián , Spain
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31
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Cole DJ, Cabeza de Vaca I, Jorgensen WL. Computation of protein-ligand binding free energies using quantum mechanical bespoke force fields. MEDCHEMCOMM 2019; 10:1116-1120. [PMID: 31391883 PMCID: PMC6644397 DOI: 10.1039/c9md00017h] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2019] [Accepted: 02/26/2019] [Indexed: 12/17/2022]
Abstract
A quantum mechanical bespoke molecular mechanics force field is derived for the L99A mutant of T4 lysozyme and used to compute absolute binding free energies of six benzene analogs to the protein. Promising agreement between theory and experiment highlights the potential for future use of system-specific force fields in computer-aided drug design.
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Affiliation(s)
- Daniel J Cole
- School of Natural and Environmental Sciences , Newcastle University , Newcastle upon Tyne NE1 7RU , UK .
| | - Israel Cabeza de Vaca
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
| | - William L Jorgensen
- Department of Chemistry , Yale University , New Haven , Connecticut 06520-8107 , USA
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32
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33
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Horton JT, Allen AEA, Dodda LS, Cole DJ. QUBEKit: Automating the Derivation of Force Field Parameters from Quantum Mechanics. J Chem Inf Model 2019; 59:1366-1381. [DOI: 10.1021/acs.jcim.8b00767] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Joshua T. Horton
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Alice E. A. Allen
- TCM Group, Cavendish Laboratory, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Leela S. Dodda
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, United States
| | - Daniel J. Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
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34
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Athanasiou C, Cournia Z. From Computers to Bedside: Computational Chemistry Contributing to FDA Approval. BIOMOLECULAR SIMULATIONS IN STRUCTURE-BASED DRUG DISCOVERY 2018. [DOI: 10.1002/9783527806836.ch7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christina Athanasiou
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
| | - Zoe Cournia
- Biomedical Research Foundation; Academy of Athens; 4 Soranou Ephessiou 11527 Athens Greece
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35
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Freindorf M, Tao Y, Sethio D, Cremer D, Kraka E. New mechanistic insights into the Claisen rearrangement of chorismate – a Unified Reaction Valley Approach study. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1530464] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Marek Freindorf
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Yunwen Tao
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Daniel Sethio
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Dieter Cremer
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
| | - Elfi Kraka
- Computational and Theoretical Chemistry Group (CATCO), Department of Chemistry, Southern Methodist University, Dallas, TX, USA
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36
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Bansal RK, Gupta R, Kour M. Synergy between Experimental and Theoretical Results of Some Reactions of Annelated 1,3-Azaphospholes. Molecules 2018; 23:molecules23061283. [PMID: 29861479 PMCID: PMC6099638 DOI: 10.3390/molecules23061283] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 11/23/2022] Open
Abstract
Computational calculations have been used successfully to explain the reactivity of the >C=P- functionality in pyrido-annelated 1,3-azaphospholes. Theoretical investigation at the Density Functional Theory (DFT) level shows that the lone pair of the bridgehead nitrogen atoms is involved in extended conjugation, due to which electron density increases considerably in the five-membered azaphosphole ring. The electron density in the azaphosphole is further enhanced by the presence of an ester group at the 3-position making the >C=P- functionality electron-rich. Thus, 1,3-azaphospholo[5,1-a]pyridine, i.e., 2-phosphaindolizine having ester group at the 3-position only does not undergo Diels-Alder (DA) reaction with an electron rich diene, such as 2,3-dimethyl-1,3-butadiene (DMB). However, an ester group at 1-position acts as electron-sink, due to which transfer of the electron density to the >C=P- moiety is checked and DA reaction occurs across the >C=P- functionality. The coordination of the Lewis acid to the carbonyl group at the 3-position raises the activation barrier, while it is lowered remarkably when it is coordinated to the P atom. Furthermore, the attack of 1,3-butadiene on the Si face of the P-coordinated (o-menthoxy)aluminum dichloride complex is a lower activation energy path. Fukui functions could be used to explain relative reactivities of indolizine and 2-phosphaindolizine towards electrophilic substitution reactions.
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Affiliation(s)
- Raj K Bansal
- Department of Chemistry, The IIS University, Jaipur 302020, India.
| | - Raakhi Gupta
- Department of Chemistry, The IIS University, Jaipur 302020, India.
| | - Manjinder Kour
- Department of Chemistry, The IIS University, Jaipur 302020, India.
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37
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Culka M, Gisdon FJ, Ullmann GM. Computational Biochemistry-Enzyme Mechanisms Explored. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2017; 109:77-112. [PMID: 28683923 DOI: 10.1016/bs.apcsb.2017.04.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Understanding enzyme mechanisms is a major task to achieve in order to comprehend how living cells work. Recent advances in biomolecular research provide huge amount of data on enzyme kinetics and structure. The analysis of diverse experimental results and their combination into an overall picture is, however, often challenging. Microscopic details of the enzymatic processes are often anticipated based on several hints from macroscopic experimental data. Computational biochemistry aims at creation of a computational model of an enzyme in order to explain microscopic details of the catalytic process and reproduce or predict macroscopic experimental findings. Results of such computations are in part complementary to experimental data and provide an explanation of a biochemical process at the microscopic level. In order to evaluate the mechanism of an enzyme, a structural model is constructed which can be analyzed by several theoretical approaches. Several simulation methods can and should be combined to get a reliable picture of the process of interest. Furthermore, abstract models of biological systems can be constructed combining computational and experimental data. In this review, we discuss structural computational models of enzymatic systems. We first discuss various models to simulate enzyme catalysis. Furthermore, we review various approaches how to characterize the enzyme mechanism both qualitatively and quantitatively using different modeling approaches.
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Affiliation(s)
- Martin Culka
- Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
| | - Florian J Gisdon
- Computational Biochemistry, University of Bayreuth, Bayreuth, Germany
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38
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Fokas AS, Cole DJ, Hine NDM, Wells SA, Payne MC, Chin AW. Evidence of Correlated Static Disorder in the Fenna-Matthews-Olson Complex. J Phys Chem Lett 2017; 8:2350-2356. [PMID: 28485971 DOI: 10.1021/acs.jpclett.7b00669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Observation of excitonic quantum beats in photosynthetic antennae has prompted wide debate regarding the function of excitonic coherence in pigment-protein complexes. Much of this work focuses on the interactions of excitons with the femto-to-picosecond dynamical fluctuations of their environment. However, in experiments these effects can be masked by static disorder of the excited-state energies across ensembles, whose microscopic origins are challenging to predict. Here the excited-state properties of ∼2000 atom clusters of the Fenna-Matthews-Olson complex are simulated using a unique combination of linear-scaling density functional theory and constrained geometric dynamics. While slow, large amplitude protein motion leads to large variations in the Qy transitions of two pigments, we identify pigment-protein correlations that greatly reduce variations in the energy gap across the ensemble, which is consistent with experimental observations of suppressed inhomogeneous dephasing of quantum beats.
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Affiliation(s)
- Alexander S Fokas
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J Cole
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
- School of Chemistry, Newcastle University , Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick , Coventry CV4 7AL, United Kingdom
| | - Stephen A Wells
- Department of Chemistry, University of Bath , Claverton Down BA2 7AY, United Kingdom
| | - Michael C Payne
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Alex W Chin
- TCM Group, Cavendish Laboratory , 19 J J Thomson Avenue, Cambridge CB3 0HE, United Kingdom
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39
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Baker LA, Habershon S. Photosynthetic pigment-protein complexes as highly connected networks: implications for robust energy transport. Proc Math Phys Eng Sci 2017; 473:20170112. [PMID: 28588417 PMCID: PMC5454362 DOI: 10.1098/rspa.2017.0112] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 05/04/2017] [Indexed: 02/01/2023] Open
Abstract
Photosynthetic pigment-protein complexes (PPCs) are a vital component of the light-harvesting machinery of all plants and photosynthesizing bacteria, enabling efficient transport of the energy of absorbed light towards the reaction centre, where chemical energy storage is initiated. PPCs comprise a set of chromophore molecules, typically bacteriochlorophyll species, held in a well-defined arrangement by a protein scaffold; this relatively rigid distribution leads to a viewpoint in which the chromophore subsystem is treated as a network, where chromophores represent vertices and inter-chromophore electronic couplings represent edges. This graph-based view can then be used as a framework within which to interrogate the role of structural and electronic organization in PPCs. Here, we use this network-based viewpoint to compare excitation energy transfer (EET) dynamics in the light-harvesting complex II (LHC-II) system commonly found in higher plants and the Fenna-Matthews-Olson (FMO) complex found in green sulfur bacteria. The results of our simple network-based investigations clearly demonstrate the role of network connectivity and multiple EET pathways on the efficient and robust EET dynamics in these PPCs, and highlight a role for such considerations in the development of new artificial light-harvesting systems.
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Affiliation(s)
| | - Scott Habershon
- Department of Chemistry and Centre for Scientific Computing, University of Warwick, Coventry CV4 7AL, UK
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40
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Steinmann C, Bratholm LA, Olsen JMH, Kongsted J. Automated Fragmentation Polarizable Embedding Density Functional Theory (PE-DFT) Calculations of Nuclear Magnetic Resonance (NMR) Shielding Constants of Proteins with Application to Chemical Shift Predictions. J Chem Theory Comput 2017; 13:525-536. [PMID: 27992211 DOI: 10.1021/acs.jctc.6b00965] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Full-protein nuclear magnetic resonance (NMR) shielding constants based on ab initio calculations are desirable, because they can assist in elucidating protein structures from NMR experiments. In this work, we present NMR shielding constants computed using a new automated fragmentation (J. Phys. Chem. B 2009, 113, 10380-10388) approach in the framework of polarizable embedding density functional theory. We extend our previous work to give both basis set recommendations and comment on how large the quantum mechanical region should be to successfully compute 13C NMR shielding constants that are comparable with experiment. The introduction of a probabilistic linear regression model allows us to substantially reduce the number of snapshots that are needed to make comparisons with experiment. This approach is further improved by augmenting snapshot selection with chemical shift predictions by which we can obtain a representative subset of snapshots that gives the smallest predicted error, compared to experiment. Finally, we use this subset of snapshots to calculate the NMR shielding constants at the PE-KT3/pcSseg-2 level of theory for all atoms in the protein GB3.
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Affiliation(s)
- Casper Steinmann
- Centre for Computational Chemistry, School of Chemistry, University of Bristol , Bristol BS8 1TS, United Kingdom.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
| | | | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark , DK-5230 Odense M, Denmark
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41
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Dziedzic J, Mao Y, Shao Y, Ponder J, Head-Gordon T, Head-Gordon M, Skylaris CK. TINKTEP: A fully self-consistent, mutually polarizable QM/MM approach based on the AMOEBA force field. J Chem Phys 2016; 145:124106. [DOI: 10.1063/1.4962909] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Jacek Dziedzic
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
- Faculty of Applied Physics and Mathematics, Gdańsk University of Technology, Gdańsk, Poland
| | - Yuezhi Mao
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Yihan Shao
- Q-Chem Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, USA
| | - Jay Ponder
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Teresa Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
- Department of Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, USA
- Department of Bioengineering, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Chris-Kriton Skylaris
- School of Chemistry, University of Southampton, Highfield, Southampton SO17 1BJ, United Kingdom
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