1
|
Mrovec M, Gill PMW. How delocalized are the polyacenes? J Comput Chem 2024; 45:701-709. [PMID: 38100265 DOI: 10.1002/jcc.27258] [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: 09/30/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 12/17/2023]
Abstract
In an attempt to quantify electron delocalization in polyacenes with up to 50 carbon atoms, we have performed self-consistent field calculations in which the π electrons are constrained to occupy highly localized molecular orbitals (HILOs) centered on a maximum of two, six or ten adjacent carbon atoms. We have also performed similar calculations on simple polyacene analogs consisting only of hydrogen atoms and exhibiting electron delocalization in the σ framework. We find that the energetic cost of localizing the π electrons in the polyacenes is roughly 60, 5 or 0.1 kJ/mol per ring atom for the two-, six- and ten-atom HILOs, respectively, and the use of these localized models overestimates the predicted hydrogenation energies of the acenes by roughly 50%, 4% and 0.1%, respectively. We conclude that the chemistry of polyacenes can be modeled well using highly localized descriptions of the π electrons.
Collapse
Affiliation(s)
- Martin Mrovec
- School of Chemistry, University of Sydney, Camperdown, New South Wales, Australia
| | - Peter M W Gill
- School of Chemistry, University of Sydney, Camperdown, New South Wales, Australia
| |
Collapse
|
2
|
Xu Y, Yan X, Zheng H, Li J, Wu X, Xu J, Zhen Z, Du C. The application of encapsulation technology in the food Industry: Classifications, recent Advances, and perspectives. Food Chem X 2024; 21:101240. [PMID: 38434690 PMCID: PMC10907187 DOI: 10.1016/j.fochx.2024.101240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/31/2024] [Accepted: 02/17/2024] [Indexed: 03/05/2024] Open
Abstract
Encapsulation technology has been extensively used to enhance the stability, specificity, and bioavailability of essential food ingredients. Additionally, it plays a vital role in improving product quality and reducing production costs. This study presents a comprehensive classification of encapsulation techniques based on the state of different cores (solid, liquid, and gaseous) and offers a detailed description and analysis of these encapsulation methods. Specifically, it introduces the diverse applications of encapsulation technology in food, encompassing areas such as antioxidant, protein activity, physical stability, controlled release, delivery, antibacterial, and probiotics. The potential impact of encapsulation technology is expected to make encapsulation technology a major process and research hotspot in the food industry. Future research directions include applications of encapsulation for enzymes, microencapsulation of biosensors, and novel technologies such as self-assembly. This study provides a valuable theoretical reference for the in-depth research and wide application of encapsulation technology in the food industry.
Collapse
Affiliation(s)
- Yaguang Xu
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Xinxin Yan
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Haibo Zheng
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Jingjun Li
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Xiaowei Wu
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Jingjing Xu
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
| | - Zongyuan Zhen
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
- The Institute of Functional Agriculture (Food) Science and Technology at Yangtze River Delta (iFAST), Chuzhou 239000, China
- Anhui Provincial Key Laboratory of Functional Agriculture and Functional Food, Chuzhou 233100, China
| | - Chuanlai Du
- College of Food Engineering, Anhui Science and Technology University, Chuzhou 233100, China
- Anhui Provincial Key Laboratory of Functional Agriculture and Functional Food, Chuzhou 233100, China
| |
Collapse
|
3
|
Wieduwilt EK, Boto RA, Macetti G, Laplaza R, Contreras-García J, Genoni A. Extracting Quantitative Information at Quantum Mechanical Level from Noncovalent Interaction Index Analyses. J Chem Theory Comput 2023; 19:1063-1079. [PMID: 36656682 DOI: 10.1021/acs.jctc.2c01092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The noncovalent interaction (NCI) index is nowadays a well-known strategy to detect NCIs in molecular systems. Even though it initially provided only qualitative descriptions, the technique has been recently extended to also extract quantitative information. To accomplish this task, integrals of powers of the electron distribution were considered, with the requirement that the overall electron density can be clearly decomposed as sum of distinct fragment contributions to enable the definition of the (noncovalent) integration region. So far, this was done by only exploiting approximate promolecular electron densities, which are given by the sum of spherically averaged atomic electron distributions and thus represent too crude approximations. Therefore, to obtain more quantum mechanically (QM) rigorous results from NCI index analyses, in this work, we propose to use electron densities obtained through the transfer of extremely localized molecular orbitals (ELMOs) or through the recently developed QM/ELMO embedding technique. Although still approximate, the electron distributions resulting from the abovementioned methods are fully QM and, above all, are again partitionable into subunit contributions, which makes them completely suitable for the NCI integral approach. Therefore, we benchmarked the integrals resulting from NCI index analyses (both those based on the promolecular densities and those based on ELMO electron distributions) against interaction energies computed at a high quantum chemical level (in particular, at the coupled cluster level). The performed test calculations have indicated that the NCI integrals based on ELMO electron densities outperform the promolecular ones. Furthermore, it was observed that the novel quantitative NCI-(QM/)ELMO approach can be also profitably exploited both to characterize and evaluate the strength of specific interactions between ligand subunits and protein residues in protein-ligand complexes and to follow the evolution of NCIs along trajectories of molecular dynamics simulations. Although further methodological improvements are still possible, the new quantitative ELMO-based technique could be already exploited in situations in which fast and reliable assessments of NCIs are crucial, such as in computational high-throughput screenings for drug discovery.
Collapse
Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Roberto A Boto
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Rubén Laplaza
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Julia Contreras-García
- Laboratoire de Chimie Théorique (LCT), UMR 7616, Sorbonne Université & CNRS, 4 Place Jussieu, Paris F-75005, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| |
Collapse
|
4
|
Macetti G, Genoni A. Introduction of a weighting scheme for the X-ray restrained wavefunction approach: advantages and drawbacks. Acta Crystallogr A Found Adv 2023; 79:25-40. [PMID: 36601761 DOI: 10.1107/s2053273322010221] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Accepted: 10/23/2022] [Indexed: 11/22/2022] Open
Abstract
In a quite recent study [Genoni et al. (2017). IUCrJ, 4, 136-146], it was observed that the X-ray restrained wavefunction (XRW) approach allows a more efficient and larger capture of electron correlation effects on the electron density if high-angle reflections are not considered in the calculations. This is due to the occurrence of two concomitant effects when one uses theoretical X-ray diffraction data corresponding to a single-molecule electron density in a large unit cell: (i) the high-angle reflections are generally much more numerous than the low- and medium-angle ones, and (ii) they are already very well described at unrestrained level. Nevertheless, since high-angle data also contain important information that should not be disregarded, it is not advisable to neglect them completely. For this reason, based on the results of the previous investigation, this work introduces a weighting scheme for XRW calculations to up-weight the contribution of low- and medium-angle reflections, and, at the same time, to reasonably down-weight the importance of the high-angle data. The proposed strategy was tested through XRW computations with both theoretical and experimental structure-factor amplitudes. The tests have shown that the new weighting scheme works optimally if it is applied with theoretically generated X-ray diffraction data, while it is not advantageous when traditional experimental X-ray diffraction data (even of very high resolution) are employed. This also led to the conclusion that the use of a specific external parameter λJ for each resolution range might not be a suitable strategy to adopt in XRW calculations exploiting experimental X-ray data as restraints.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques, 1 Boulevard Arago, Metz, F-57078, France
| |
Collapse
|
5
|
Initial Maximum Overlap Method Embedded with Extremely Localized Molecular Orbitals for Core-Ionized States of Large Systems. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010136. [PMID: 36615331 PMCID: PMC9822432 DOI: 10.3390/molecules28010136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/21/2022] [Accepted: 12/22/2022] [Indexed: 12/28/2022]
Abstract
Despite great advances in X-ray absorption spectroscopy for the investigation of small molecule electronic structure, the application to biosystems of experimental techniques developed within this research field remains a challenge. To partially circumvent the problem, users resort to theoretical methods to interpret or predict the X-ray absorption spectra of large molecules. To accomplish this task, only low-cost computational strategies can be exploited. For this reason, some of them are single Slater determinant wavefunction approaches coupled with multiscale embedding techniques designed to treat large systems of biological interest. Therefore, in this work, we propose to apply the recently developed IMOM/ELMO embedding method to the determination of core-ionized states. The IMOM/ELMO technique resulted from the combination of the single Slater determinant Δself-consistent-field-initial maximum overlap approach (ΔSCF-IMOM) with the QM/ELMO (quantum mechanics/extremely localized molecular orbital) embedding strategy, a method where only the chemically relevant region of the examined system is treated at fully quantum chemical level, while the rest is described through transferred and frozen extremely localized molecular orbitals (ELMOs). The IMOM/ELMO technique was initially validated by computing core-ionization energies for small molecules, and it was afterwards exploited to study larger biosystems. The obtained results are in line with those reported in previous studies that applied alternative ΔSCF approaches. This makes us envisage a possible future application of the proposed method to the interpretation of X-ray absorption spectra of large molecules.
Collapse
|
6
|
Chodkiewicz ML, Gajda R, Lavina B, Tkachev S, Prakapenka VB, Dera P, Wozniak K. Accurate crystal structure of ice VI from X-ray diffraction with Hirshfeld atom refinement. IUCRJ 2022; 9:573-579. [PMID: 36071798 PMCID: PMC9438488 DOI: 10.1107/s2052252522006662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 06/28/2022] [Indexed: 06/15/2023]
Abstract
Water is an essential chemical compound for living organisms, and twenty of its different crystal solid forms (ices) are known. Still, there are many fundamental problems with these structures such as establishing the correct positions and thermal motions of hydrogen atoms. The list of ice structures is not yet complete as DFT calculations have suggested the existence of additional and - to date - unknown phases. In many ice structures, neither neutron diffraction nor DFT calculations nor X-ray diffraction methods can easily solve the problem of hydrogen atom disorder or accurately determine their anisotropic displacement parameters (ADPs). Here, accurate crystal structures of H2O, D2O and mixed (50%H2O/50%D2O) ice VI obtained by Hirshfeld atom refinement (HAR) of high-pressure single-crystal synchrotron and laboratory X-ray diffraction data are presented. It was possible to obtain O-H/D bond lengths and ADPs for disordered hydrogen atoms which are in good agreement with the corresponding single-crystal neutron diffraction data. These results show that HAR combined with X-ray diffraction can compete with neutron diffraction in detailed studies of polymorphic forms of ice and crystals of other hydrogen-rich compounds. As neutron diffraction is relatively expensive, requires larger crystals which can be difficult to obtain and access to neutron facilities is restricted, cheaper and more accessible X-ray measurements combined with HAR can facilitate the verification of the existing ice polymorphs and the quest for new ones.
Collapse
Affiliation(s)
- Michal L. Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa 02-089, Poland
| | - Roman Gajda
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa 02-089, Poland
| | - Barbara Lavina
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Sergey Tkachev
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Lemont, IL 60439, USA
| | - Vitali B. Prakapenka
- Hawai’i Institute of Geophysics and Planetology, Université d’hawaï à mānoa, 1680 East-West Road, Honolulu, HI 96822, USA
| | - Przemyslaw Dera
- Hawai’i Institute of Geophysics and Planetology, Université d’hawaï à mānoa, 1680 East-West Road, Honolulu, HI 96822, USA
| | - Krzysztof Wozniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury, Warszawa 02-089, Poland
| |
Collapse
|
7
|
Zhang Y, Qi J, Zhou R, Yang M. A Polarizable Fragment Density Model and Its Applications. J Chem Phys 2022; 157:084108. [DOI: 10.1063/5.0101437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work presented a new model, Polarizable Fragment Density Model (PFDM), for the fast energy estimation of peptides, proteins or other large molecular systems. By introducing an analogous relation to the Virial theorem, the kinetic energy in Kohn-Sham Density Functional Theory (KS-DFT) is approximated to the corresponding potential energy multiplied by a scale factor. Furthermore, the error due to this approximation together with the exchange-correlation energy is approximated as a second order Taylor's expansion about density. The PFDM energy is expressed as a functional of electronic density with system-dependent model parameters which are a scaling factor c and a series of atomic pairwise KAB. The electron density in PFDM consists of a frozen part retaining chemical bonding information and a polarizable part to describe polarization effects, both of which are expanded as a linear expansion of Gaussian basis functions. The frozen density can be pre-calculated by fitting the DFT calculated density of fragments as well as the polarizable density is optimized to solve PFDM energy. The PFDM energy is a quadratic function of the expansion coefficients of polarizable density and can be solved without expensive iteration process and numerical integrals. PFDM is especially suitable for the energy calculation of large molecular system with identical subunits, such as proteins, nucleic acids and molecular clusters. Applying the PFDM method to the proteins, the results show that the accuracy is comparable to the PM6 semi-empirical method, and the efficiency is one order of magnitude faster than PM6.
Collapse
Affiliation(s)
- Yingfeng Zhang
- Chinese Academy of Sciences Wuhan Institute of Physics and Mathematics, China
| | - Ji Qi
- Wuhan Institute of Physics and Mathematics,Chinese Academy of Sciences, China
| | - Rui Zhou
- Chinese Academy of Sciences Wuhan Institute of Physics and Mathematics, China
| | - Minghui Yang
- Chinese Academy of Sciences Wuhan Institute of Physics and Mathematics, China
| |
Collapse
|
8
|
Hu X, Luo M, ur Rehman M, Sun J, Yaseen HA, Irshad F, Zhao Y, Wang S, Ma X. Mechanistic insight into the electron-donation effect of modified ZIF-8 on Ru for CO2 hydrogenation to formic acid. J CO2 UTIL 2022. [DOI: 10.1016/j.jcou.2022.101992] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
|
9
|
Chodkiewicz M, Pawlędzio S, Woińska M, Woźniak K. Fragmentation and transferability in Hirshfeld atom refinement. IUCRJ 2022; 9:298-315. [PMID: 35371499 PMCID: PMC8895009 DOI: 10.1107/s2052252522000690] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Accepted: 01/19/2022] [Indexed: 05/06/2023]
Abstract
Hirshfeld atom refinement (HAR) is one of the most effective methods for obtaining accurate structural parameters for hydrogen atoms from X-ray diffraction data. Unfortunately, it is also relatively computationally expensive, especially for larger molecules due to wavefunction calculations. Here, a fragmentation approach has been tested as a remedy for this problem. It gives an order of magnitude improvement in computation time for larger organic systems and is a few times faster for metal-organic systems at the cost of only minor differences in the calculated structural parameters when compared with the original HAR calculations. Fragmentation was also applied to polymeric and disordered systems where it provides a natural solution to problems that arise when HAR is applied. The concept of fragmentation is closely related to the transferable aspherical atom model (TAAM) and allows insight into possible ways to improve TAAM. Hybrid approaches combining fragmentation with the transfer of atomic densities between chemically similar atoms have been tested. An efficient handling of intermolecular interactions was also introduced for calculations involving fragmentation. When applied in fragHAR (a fragmentation approach for polypeptides) as a replacement for the original approach, it allowed for more efficient calculations. All of the calculations were performed with a locally modified version of Olex2 combined with a development version of discamb2tsc and ORCA. Care was taken to efficiently use the power of multicore processors by simple implementation of load-balancing, which was found to be very important for lowering computational time.
Collapse
Affiliation(s)
- Michał Chodkiewicz
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Sylwia Pawlędzio
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Magdalena Woińska
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| | - Krzysztof Woźniak
- Biological and Chemical Research Centre, Department of Chemistry, University of Warsaw, Żwirki i Wigury 101, Warszawa 02-089, Poland
| |
Collapse
|
10
|
Goletto L, Kjønstad EF, Folkestad SD, Høyvik IM, Koch H. Linear-Scaling Implementation of Multilevel Hartree-Fock Theory. J Chem Theory Comput 2021; 17:7416-7427. [PMID: 34747179 PMCID: PMC8675138 DOI: 10.1021/acs.jctc.1c00299] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce a new algorithm for the construction of the two-electron contributions to the Fock matrix in multilevel Hartree-Fock (MLHF) theory. In MLHF, the density of an active molecular region is optimized, while the density of an inactive region is fixed. The MLHF equations are solved in a reduced molecular orbital (MO) basis localized to the active region. The locality of the MOs can be exploited to reduce the computational cost of the Fock matrix: the cost related to the inactive density becomes linear scaling, while the iterative cost related to the active density is independent of the system size. We demonstrate the performance of this new algorithm on a variety of systems, including amino acid chains, water clusters, and solvated systems.
Collapse
Affiliation(s)
- Linda Goletto
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Eirik F Kjønstad
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Sarai D Folkestad
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Ida-Marie Høyvik
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway
| | - Henrik Koch
- Department of Chemistry, Norwegian University of Science and Technology, Trondheim 7491, Norway.,Scuola Normale Superiore, Pisa 56126, Italy
| |
Collapse
|
11
|
Macetti G, Genoni A. Initial Maximum Overlap Method for Large Systems by the Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Technique. J Chem Theory Comput 2021; 17:4169-4182. [PMID: 34196174 DOI: 10.1021/acs.jctc.1c00388] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Quantum chemistry offers a large variety of methods to treat excited states. Many of them are based on a multireference wave function ansatz and are therefore characterized by an intrinsic complexity and high computational costs. To overcome these drawbacks and also some limitations of simpler single-reference approaches (e.g., configuration interaction singles and time-dependent density functional theory), the single-determinant Δself-consistent field-initial maximum overlap method (ΔSCF-IMOM) has been proposed. This strategy substitutes the aufbau principle with a criterion that occupies molecular orbitals at successive SCF iterations on the basis of their maximum overlap with a proper set of guess orbitals for the target excited state. In this way, it prevents the SCF process to collapse to the ground state wave function and provides excited state single Slater determinant solutions to the SCF equations. Here, we propose to extend the applicability of the IMOM to the treatment of localized excited states of large systems. To accomplish this task, we coupled it with the QM/ELMO (quantum mechanics/extremely localized molecular orbitals) strategy, a quantum mechanical embedding method in which the most chemically relevant part of the system is treated with traditional quantum chemical approaches, while the rest is described by extremely localized molecular orbitals transferred from recently constructed libraries or proper model molecules. After presenting the theoretical foundations of the new IMOM/ELMO technique, in this paper, we will show and discuss the results of preliminary test calculations carried out on both model systems (i.e., decanoic acid, decene, decapentaene, and solvated acrolein) and a system of biological interest (flavin mononucleotide in the flavodoxin protein). We observed that, for localized excited states, the new IMOM/ELMO method provides reliable results, and it reproduces the outcomes of fully IMOM calculations within the chemical accuracy threshold (i.e., 0.043 eV) by including only a limited number of atoms in the QM region. Furthermore, the first application of our embedding technique to a larger biological system gave completely plausible results in line with those obtained through more traditional quantum mechanical methods, thus opening the possibility of using the new approach in future investigations of photobiology problems.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
12
|
Macetti G, Genoni A. Three-Layer Multiscale Approach Based on Extremely Localized Molecular Orbitals to Investigate Enzyme Reactions. J Phys Chem A 2021; 125:6013-6027. [PMID: 34190569 DOI: 10.1021/acs.jpca.1c05040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanics/molecular mechanics (QM/MM) calculations are widely used embedding techniques to computationally investigate enzyme reactions. In most QM/MM computations, the quantum mechanical region is treated through density functional theory (DFT), which offers the best compromise between chemical accuracy and computational cost. Nevertheless, to obtain more accurate results, one should resort to wave function-based methods, which however lead to a much larger computational cost already for relatively small QM subsystems. To overcome this drawback, we propose the coupling of our QM/ELMO (quantum mechanics/extremely localized molecular orbital) approach with molecular mechanics, thus introducing the three-layer QM/ELMO/MM technique. The QM/ELMO strategy is an embedding method in which the chemically relevant part of the system is treated at the quantum mechanical level, while the rest is described through frozen ELMOs. Since the QM/ELMO method reproduces results of fully QM computations within chemical accuracy and with a much lower computational effort, it can be considered a suitable strategy to extend the range of applicability and accuracy of the QM/MM scheme. In this paper, other than briefly presenting the theoretical bases of the QM/ELMO/MM technique, we will also discuss its validation on the well-tested deprotonation of acetyl coenzyme A by aspartate in citrate synthase.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
13
|
Yan Z, Li X, Chung LW. Multiscale Quantum Refinement Approaches for Metalloproteins. J Chem Theory Comput 2021; 17:3783-3796. [PMID: 34032440 DOI: 10.1021/acs.jctc.1c00148] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Biomolecules with metal ion(s) (e.g., metalloproteins) play many important biological roles. However, accurate structural determination of metalloproteins, particularly those containing transition metal ion(s), is challenging due to their complicated electronic structure, complex bonding of metal ions, and high number of conformations in biomolecules. Quantum refinement, which was proposed to combine crystallographic data with computational chemistry methods by several groups, can improve the local structures of some proteins. In this study, a quantum refinement method combining several multiscale computational schemes with experimental (X-ray diffraction) information was developed for metalloproteins. Various quantum refinement approaches using different ONIOM (our own N-layered integrated molecular orbital and molecular mechanics) combinations of quantum mechanics (QM), semiempirical (SE), and molecular mechanics (MM) methods were conducted to assess the performance and reliability on the refined local structure in two metalloproteins. The structures for two (Cu- or Zn-containing) metalloproteins were refined by combining two-layer ONIOM2(QM1/QM2) and ONIOM2(QM/MM) and three-layer ONIOM3(QM1/QM2/MM) schemes with experimental data. The accuracy of the quantum-refined metal binding sites was also examined and compared in these multiscale quantum refinement calculations. ONIOM3(QM/SE/MM) schemes were found to give good results with lower computational costs and were proposed to be a good choice for the multiscale computational scheme for quantum refinement calculations of metal binding site(s) in metalloproteins with high efficiency. Additionally, a two-center ONIOM approach was employed to speed up the quantum refinement calculations for the Zn metalloprotein with two remote active sites/ligands. Moreover, a recent quantum-embedding wavefunction-in-density functional theory (WF-in-DFT) method was also adopted as the high-level method in unprecedented ONIOM2(CCSD-in-B3LYP/MM) and ONIOM3(CCSD-in-B3LYP/SE/MM) calculations, which can be regarded as novel pseudo-three- and pseudo-four-layer ONIOM methods, respectively, to refine the key Zn binding site at the coupled-cluster singles and doubles (CCSD) level. These refined results indicate that multiscale quantum refinement schemes can be used to improve the structural accuracy obtained for local metal binding site(s) in metalloproteins with high efficiency.
Collapse
Affiliation(s)
- Zeyin Yan
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Xin Li
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| | - Lung Wa Chung
- Shenzhen Grubbs Institute, Department of Chemistry and Guangdong Provincial Key Laboratory of Catalysis, Southern University of Science and Technology, Shenzhen 518055, China
| |
Collapse
|
14
|
Malaspina LA, Genoni A, Jayatilaka D, Turner MJ, Sugimoto K, Nishibori E, Grabowsky S. The advanced treatment of hydrogen bonding in quantum crystallography. J Appl Crystallogr 2021; 54:718-729. [PMID: 34188611 PMCID: PMC8202034 DOI: 10.1107/s1600576721001126] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 01/31/2021] [Indexed: 11/16/2022] Open
Abstract
Although hydrogen bonding is one of the most important motifs in chemistry and biology, H-atom parameters are especially problematic to refine against X-ray diffraction data. New developments in quantum crystallography offer a remedy. This article reports how hydrogen bonds are treated in three different quantum-crystallographic methods: Hirshfeld atom refinement (HAR), HAR coupled to extremely localized molecular orbitals and X-ray wavefunction refinement. Three different compound classes that form strong intra- or intermolecular hydrogen bonds are used as test cases: hydrogen maleates, the tripeptide l-alanyl-glycyl-l-alanine co-crystallized with water, and xylitol. The differences in the quantum-mechanical electron densities underlying all the used methods are analysed, as well as how these differences impact on the refinement results.
Collapse
Affiliation(s)
- Lorraine A. Malaspina
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| | - Alessandro Genoni
- Université de Lorraine and CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, 57078 Metz, France
| | - Dylan Jayatilaka
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Michael J. Turner
- The University of Western Australia, School of Molecular Sciences, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Kunihisa Sugimoto
- Japan Synchrotron Radiation Research Institute/Diffraction and Scattering Division, 1-1-1 Kouto, Sayo-cho, Sayo-gun, Hyogo 679-5198, Japan
- Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida-Ushinomiya-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Eiji Nishibori
- Department of Physics, Faculty of Pure and Applied Sciences, Tsukuba Research Center for Energy Materials Science (TREMS), University of Tsukuba, Tsukuba, Japan
| | - Simon Grabowsky
- Universität Bern, Departement für Chemie, Biochemie und Pharmazie, Freiestrasse 3, 3012 Bern, Switzerland
- Universität Bremen, Fachbereich 2 – Biologie/Chemie, Institut für Anorganische Chemie und Kristallographie, Leobener Strasse 3, 28359 Bremen, Germany
| |
Collapse
|
15
|
Macetti G, Wieduwilt EK, Genoni A. QM/ELMO: A Multi-Purpose Fully Quantum Mechanical Embedding Scheme Based on Extremely Localized Molecular Orbitals. J Phys Chem A 2021; 125:2709-2726. [DOI: 10.1021/acs.jpca.0c11450] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K. Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
16
|
Wieduwilt EK, Macetti G, Genoni A. Climbing Jacob's Ladder of Structural Refinement: Introduction of a Localized Molecular Orbital-Based Embedding for Accurate X-ray Determinations of Hydrogen Atom Positions. J Phys Chem Lett 2021; 12:463-471. [PMID: 33369421 DOI: 10.1021/acs.jpclett.0c03421] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
The positions of hydrogen atoms in molecules are fundamental in many aspects of chemistry. Nevertheless, most molecular structures are obtained from refinements of X-ray data exploiting the independent atom model (IAM), which uses spherical atomic densities and provides bond lengths involving hydrogen atoms that are too short compared to the neutron reference values. To overcome the IAM shortcomings, the wave function-based Hirshfeld atom refinement (HAR) method has been recently proposed, emerging as a promising strategy able to give element-hydrogen bond distances in excellent agreement with the neutron ones in terms of accuracy and precision. In this Letter, we propose a significant improvement of HAR based on the idea of describing the crystal environment explicitly in the underlying wave function calculation through a quantum mechanical embedding strategy that exploits extremely localized molecular orbitals. Test-bed refinements on a crystal structure characterized by strong intermolecular interactions are also discussed.
Collapse
Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
17
|
Wieduwilt EK, Boisson JC, Terraneo G, Hénon E, Genoni A. A Step toward the Quantification of Noncovalent Interactions in Large Biological Systems: The Independent Gradient Model-Extremely Localized Molecular Orbital Approach. J Chem Inf Model 2021; 61:795-809. [PMID: 33444021 DOI: 10.1021/acs.jcim.0c01188] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The independent gradient model (IGM) is a recent electron density-based computational method that enables to detect and quantify covalent and noncovalent interactions. When applied to large systems, the original version of the technique still relies on promolecular electron densities given by the sum of spherically averaged atomic electron distributions, which leads to approximate evaluations of the inter- and intramolecular interactions occurring in systems of biological interest. To overcome this drawback and perform IGM analyses based on quantum mechanically rigorous electron densities also for macromolecular systems, we coupled the IGM approach with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) that allow fast and reliable reconstructions of polypeptide and protein electron densities. The validation tests performed on small polypeptides and peptide dimers have shown that the novel IGM-ELMO strategy provides results that are systematically closer to the fully quantum mechanical ones and outperforms the IGM method based on the crude promolecular approximation, but still keeping a quite low computational cost. The results of the test calculations carried out on proteins have also confirmed the trends observed for the IGM analyses conducted on small systems. This makes us envisage the future application of the novel IGM-ELMO approach to unravel complicated noncovalent interaction networks (e.g., in protein-protein contacts) or to rationally design new drugs through molecular docking calculations and virtual high-throughput screenings.
Collapse
Affiliation(s)
- Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| | - Jean-Charles Boisson
- CReSTIC EA 3804, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Giancarlo Terraneo
- Laboratory of Supramolecular and Bio-Nanomaterials (SupraBioNanoLab), Department of Chemistry, Materials and Chemical Engineering "Giulio Natta", Politecnico di Milano, Via L. Mancinelli 7, Milan I-20131, Italy
| | - Eric Hénon
- Institut de Chimie Moléculaire de Reims UMR CNRS 7312, Université de Reims Champagne-Ardenne, Moulin de la Housse, Reims Cedex 02 BP39, F-51687, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques, UMR CNRS 7019, 1 Boulevard Arago, Metz F-57078, France
| |
Collapse
|
18
|
Quantum mechanics/extremely localized molecular orbital embedding technique: Theoretical foundations and further validation. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
19
|
Affiliation(s)
- Piero Macchi
- Department, Chemistry, Materials and Chemical Engineering, Politecnico di Milano, Milano, Italy
- Center for Nano Science and Technology CNST@polimi, Italian Institute of Technology, Milano, Italy
| |
Collapse
|
20
|
Macetti G, Genoni A. Quantum Mechanics/Extremely Localized Molecular Orbital Embedding Strategy for Excited States: Coupling to Time-Dependent Density Functional Theory and Equation-of-Motion Coupled Cluster. J Chem Theory Comput 2020; 16:7490-7506. [PMID: 33241930 DOI: 10.1021/acs.jctc.0c00956] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The QM/ELMO (quantum mechanics/extremely localized molecular orbital) method is a recently developed embedding technique in which the most important region of the system under examination is treated at fully quantum mechanical level, while the rest is described by means of transferred and frozen extremely localized molecular orbitals. In this paper, we propose the first application of the QM/ELMO approach to the investigation of excited states, and, in particular, we present the coupling of the QM/ELMO philosophy with Time-Dependent Density Functional Theory (TDDFT) and Equation-of-Motion Coupled Cluster with single and double substitutions (EOM-CCSD). The proposed TDDFT/ELMO and EOM-CCSD/ELMO strategies underwent a series of preliminary tests that were already considered for the validation of other embedding methods for excited states. The obtained results showed that the novel techniques allow the accurate description of localized excitations in large systems by only including a relatively small number of atoms in the region treated at fully quantum chemical level. Furthermore, for TDDFT/ELMO, it was also observed that (i) the method enables to avoid the presence of artificial low-lying charge-transfer states that may affect traditional TDDFT calculations, even using functionals that do not take into account long-range corrections, and (ii) the novel approach can be also successfully exploited to investigate local electronic transitions in quite large systems (e.g., reduced model of the Green Fluorescent Protein), and the accuracy of the results can be improved by including a sufficient number of chemically crucial fragments/residues in the quantum mechanical region. Finally, concerning EOM-CCSD/ELMO, it was also seen that, despite the quite crude approximation of an embedding potential given by frozen extremely localized molecular orbitals, the new strategy is able to satisfactorily account for the effects of the environment. This work paves the way to further extensions of the QM/ELMO philosophy for the study of local excitations in extended systems, suggesting the coupling of the QM/ELMO approach with other quantum chemical strategies for excited states, from the simplest ΔSCF techniques to the most advanced and computationally expensive multireferences methods.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
21
|
McCoy AB. Virtual Issue on New Tools and Methods in Physical Chemistry Research. J Phys Chem A 2020; 124:4323-4324. [PMID: 32493016 DOI: 10.1021/acs.jpca.0c04262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anne B McCoy
- Department of Chemistry, University of Washington, Seattle, Washington 98195, United States
| |
Collapse
|
22
|
Abstract
In this review article, we report on the recent progresses in the field of quantum crystallography that has witnessed a massive increase of production coupled with a broadening of the scope in the last decade. It is shown that the early thoughts about extracting quantum mechanical information from crystallographic experiments are becoming reality, although a century after prediction. While in the past the focus was mainly on electron density and related quantities, the attention is now shifting toward determination of wavefunction from experiments, which enables an exhaustive determination of the quantum mechanical functions and properties of a system. Nonetheless, methods based on electron density modelling have evolved and are nowadays able to reconstruct tiny polarizations of core electrons, coupling charge and spin models, or determining the quantum behaviour at extreme conditions. Far from being routine, these experimental and computational results should be regarded with special attention by scientists for the wealth of information on a system that they actually contain.
Collapse
|
23
|
Post-Hartree-Fock methods for Hirshfeld atom refinement: are they necessary? Investigation of a strongly hydrogen-bonded molecular crystal. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127934] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
|
24
|
Ernst M, Genoni A, Macchi P. Analysis of crystal field effects and interactions using X-ray restrained ELMOs. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.127975] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
|
25
|
Bensberg M, Neugebauer J. Orbital Alignment for Accurate Projection-Based Embedding Calculations along Reaction Paths. J Chem Theory Comput 2020; 16:3607-3619. [DOI: 10.1021/acs.jctc.0c00104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Moritz Bensberg
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 40, 48149 Münster, Germany
| |
Collapse
|
26
|
Macetti G, Wieduwilt EK, Assfeld X, Genoni A. Localized Molecular Orbital-Based Embedding Scheme for Correlated Methods. J Chem Theory Comput 2020; 16:3578-3596. [PMID: 32369363 DOI: 10.1021/acs.jctc.0c00084] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Embedding strategies currently provide the best compromise between accuracy and computational cost in modeling chemical properties and processes of large and complex systems. In this framework, different methods have been proposed all over the years, from the very popular QM/MM approaches to the more recent and very promising density matrix and density functional embedding techniques. Here, we present a further development of the quantum mechanics/extremely localized molecular orbital technique (QM/ELMO) method, a recently proposed multiscale embedding strategy in which the chemically active region of the investigated system is treated at a fully quantum mechanical level, while the rest is described by frozen extremely localized molecular orbitals previously transferred from proper libraries or tailor-made model molecules. In particular, in this work we discuss and assess in detail the extension of the QM/ELMO approach to density functional theory and post-Hartree-Fock techniques by evaluating its performances when it is used to describe chemical reactions, bond dissociations, and intermolecular interactions. The preliminary test calculations have shown that, in the investigated cases, the new embedding strategy enables the results of the corresponding fully quantum mechanical computations to be reproduced within chemical accuracy in almost all the cases but with a significantly reduced computational cost, especially when correlated post-Hartree-Fock strategies are used to describe the quantum mechanical subsystem. In light of the obtained results, we already envisage the future application of the new correlated QM/ELMO techniques to the investigation of more challenging problems, such as the modeling of enzyme catalysis, the study of excited states of biomolecules, and the refinement of macromolecular X-ray crystal structures.
Collapse
Affiliation(s)
- Giovanni Macetti
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Erna K Wieduwilt
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| | - Xavier Assfeld
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, Boulevard des Aiguilletes, BP 70239, F-54506 Vandoeuvre-lès-Nancy, France
| | - Alessandro Genoni
- Université de Lorraine & CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT), UMR CNRS 7019, 1 Boulevard Arago, F-57078 Metz, France
| |
Collapse
|
27
|
Malaspina LA, Wieduwilt EK, Bergmann J, Kleemiss F, Meyer B, Ruiz-López MF, Pal R, Hupf E, Beckmann J, Piltz RO, Edwards AJ, Grabowsky S, Genoni A. Fast and Accurate Quantum Crystallography: From Small to Large, from Light to Heavy. J Phys Chem Lett 2019; 10:6973-6982. [PMID: 31633355 DOI: 10.1021/acs.jpclett.9b02646] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The coupling of the crystallographic refinement technique Hirshfeld atom refinement (HAR) with the recently constructed libraries of extremely localized molecular orbitals (ELMOs) gives rise to the new quantum-crystallographic method HAR-ELMO. This method is significantly faster than HAR but as accurate and precise, especially concerning the free refinement of hydrogen atoms from X-ray diffraction data, so that the first fully quantum-crystallographic refinement of a protein is presented here. However, the promise of HAR-ELMO exceeds large molecules and protein crystallography. In fact, it also renders possible electron-density investigations of heavy elements in small molecules and facilitates the detection and isolation of systematic errors from physical effects.
Collapse
Affiliation(s)
- Lorraine A Malaspina
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Erna K Wieduwilt
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Justin Bergmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Florian Kleemiss
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Benjamin Meyer
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Manuel F Ruiz-López
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| | - Rumpa Pal
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Emanuel Hupf
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Jens Beckmann
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
| | - Ross O Piltz
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Alison J Edwards
- Australian Nuclear Science and Technology Organisation , Australian Centre for Neutron Scattering , New Illawarra Road , Lucas Heights , NSW 2234 , Australia
| | - Simon Grabowsky
- Institut für Anorganische Chemie und Kristallographie, Fachbereich 2 - Biologie/Chemie , Universität Bremen , Leobener Straße 3 und 7 , 28359 Bremen , Germany
- Departement für Chemie und Biochemie , Universität Bern , Freiestrasse 3 , 3012 Bern , Switzerland
| | - Alessandro Genoni
- Université de Lorraine , CNRS, Laboratoire de Physique et Chimie Théoriques (LPCT) , 1 Boulevard Arago , 57078 Metz , France
| |
Collapse
|