1
|
Deng Z, Liu C, Li Z, Zhang Y. An efficient method by combining different basis sets and SAPT levels. J Comput Chem 2024; 45:1936-1944. [PMID: 38703182 DOI: 10.1002/jcc.27386] [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: 11/13/2023] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 05/06/2024]
Abstract
In symmetry-adapted perturbation theory (SAPT), accurate calculations on non-covalent interaction (NCI) for large complexes with more than 50 atoms are time-consuming using large basis sets. More efficient ones with smaller basis sets usually result in poor prediction in terms of dispersion and overall energies. In this study, we propose two composite methods with baseline calculated at SAPT2/aug-cc-pVDZ and SAPT2/aug-cc-pVTZ with dispersion term corrected at SAPT2+ level using bond functions and smaller basis set with δ MP2 corrections respectively. Benchmark results on representative NCI data sets, such as S22, S66, and so forth, show significant improvements on the accuracy compared to the original SAPT Silver standard and comparable to SAPT Gold standard in some cases with much less computational cost.
Collapse
Affiliation(s)
- Zhihao Deng
- Beijing StoneWise Technology Co Ltd., Beijing, China
| | - Chang Liu
- Beijing StoneWise Technology Co Ltd., Beijing, China
| | - Zhongwei Li
- Yantai Gogetter Technology Co Ltd., Yantai, China
| | | |
Collapse
|
2
|
Gregory KP, Wanless EJ, Webber GB, Craig VSJ, Page AJ. A first-principles alternative to empirical solvent parameters. Phys Chem Chem Phys 2024. [PMID: 38988220 DOI: 10.1039/d4cp01975j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
Abstract
The use of solvents is ubiquitous in chemistry. Empirical parameters, such as the Kamlet-Taft parameters and Gutmann donor/acceptor numbers, have long been used to predict and quantify the effects solvents have on chemical phenomena. Collectively however, such parameters are unsatisfactory, since each describes ultimately the same non-covalent solute-solvent and solute-solute interactions in completely disparate ways. Here we hypothesise that empirical solvent parameters are essentially proxy measures of the electrostatic terms that dominate solvent-solute interactions. On the basis of this hypothesis, we develop a new fundamental descriptor of these interactions, , and show that it is a self-consistent, probe-free, first principles alternative to established empirical solvent parameters.
Collapse
Affiliation(s)
- Kasimir P Gregory
- Discipline of Chemistry, College of Engineering, Science & Environment, University of Newcastle, Callaghan 2308, Australia.
- Research School of Materials Physics, Research School of Physics, Australian National University, ACT 0200, Australia
- Division of Biomedical Science and Biochemistry, Research School of Biology, The Australian National University, Canberra, ACT 0200, Australia
| | - Erica J Wanless
- Discipline of Chemistry, College of Engineering, Science & Environment, University of Newcastle, Callaghan 2308, Australia.
| | - Grant B Webber
- Discipline of Chemical Engineering, College of Engineering, Science & Environment, University of Newcastle, Callaghan 2308, Australia
| | - Vincent S J Craig
- Research School of Materials Physics, Research School of Physics, Australian National University, ACT 0200, Australia
| | - Alister J Page
- Discipline of Chemistry, College of Engineering, Science & Environment, University of Newcastle, Callaghan 2308, Australia.
| |
Collapse
|
3
|
Bovolenta GM, Silva-Vera G, Bovino S, Molpeceres G, Kästner J, Vogt-Geisse S. In-depth exploration of catalytic sites on amorphous solid water: I. The astrosynthesis of aminomethanol. Phys Chem Chem Phys 2024; 26:18692-18706. [PMID: 38922674 DOI: 10.1039/d4cp01865f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/27/2024]
Abstract
Chemical processes taking place on ice-grain mantles are pivotal to the complex chemistry of interstellar environments. In this study, we conducted a comprehensive analysis of the catalytic effects of an amorphous solid water (ASW) surface on the reaction between ammonia (NH3) and formaldehyde (H2CO) to form aminomethanol (NH2CH2OH) using density functional theory. We identified potential catalytic sites based on the binding energy distribution of NH3 and H2CO reactants, on a set-of-clusters surface model composed of 22 water molecules and found a total of 14 reaction paths. Our results indicate that the catalytic sites can be categorized into four groups, depending on the interactions of the carbonyl oxygen and the amino group with the ice surface in the reactant complex. A detailed analysis of the reaction mechanism using Intrinsic Reaction Coordinate and reaction force analysis, revealed three distinct chemical events for this reaction: formation of the C-N bond, breaking of the N-H bond, and formation of the O-H hydroxyl bond. Depending on the type of catalytic site, these events can occur within a single, concerted, albeit asynchronous, step, or can be isolated in a step-wise mechanism, with the lowest overall transition state energy observed at 1.3 kcal mol-1. A key requirement for the low-energy mechanism is the presence of a pair of dangling OH bonds on the surface, found at 5% of the potential catalytic sites on an ASW porous surface.
Collapse
Affiliation(s)
- Giulia M Bovolenta
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
- Atomistic Simulations, Italian Institute of Technology, 16152 Genova, Italy
| | - Gabriela Silva-Vera
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
| | - Stefano Bovino
- Chemistry Department, Sapienza University of Rome, P.le A. Moro, 00185 Rome, Italy
- INAF - Osservatorio Astrofisico di Arcetri, Largo E. Fermi 5, 50125 Firenze, Italy
- Departamento de Astronomía, Facultad de Ciencias Físicas y Matemáticas, Universidad de Concepción, Av. Esteban Iturra s/n Barrio Universitario, Concepción, Chile
| | - German Molpeceres
- Departamento de Astrofísica Molecular Instituto de Física Fundamental (IFF-CSIC), Madrid, Spain
| | - Johannes Kästner
- Institute for Theoretical Chemistry, University of Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Stefan Vogt-Geisse
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile.
| |
Collapse
|
4
|
Nikitin A, Wang F. Simulation of Linear and Cyclic Alkanes with Second-Order Møller-Plesset Perturbation Theory through Adaptive Force Matching. J Chem Theory Comput 2024; 20:5241-5249. [PMID: 38848512 PMCID: PMC11209940 DOI: 10.1021/acs.jctc.4c00509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 05/28/2024] [Accepted: 05/29/2024] [Indexed: 06/09/2024]
Abstract
Predicting ensemble properties, such as density and heat of vaporization, of small hydrocarbons is challenging due to the dispersion-dominated weak interactions between these molecules. With the adaptive force matching (AFM) method, the bonded and short-range nonbonded interactions are fitted to second-order Møller-Plesset perturbation theory (MP2) references computed with the def2-TZVP basis set. The dispersion is modeled using symmetry adapted perturbation theory (SAPT) at MP4 accuracy using the def2-TZVPD basis set. A new charge matrix decomposition technique is described to obtain partial charges in AFM. Although the models developed do not have any empirical parameters, several properties of the resulting models are compared with experiments as validations. The density, heat of vaporization, pressure dependence of density, diffusion constants, and surface tensions all show quantitative agreement with experiments. Although the density shows a very small systematic error, which could be due to missing three-body dispersion, the heat of vaporization agrees with experiments of within 0.5%. The paper shows that AFM can be used as a reliable tool to enable simulations at post-Hartree-Fock quality at the cost of molecular mechanics force fields.
Collapse
Affiliation(s)
- Alexei Nikitin
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Wang
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| |
Collapse
|
5
|
Rocca D, Cortes CL, Gonthier JF, Ollitrault PJ, Parrish RM, Anselmetti GL, Degroote M, Moll N, Santagati R, Streif M. Reducing the Runtime of Fault-Tolerant Quantum Simulations in Chemistry through Symmetry-Compressed Double Factorization. J Chem Theory Comput 2024; 20:4639-4653. [PMID: 38788209 DOI: 10.1021/acs.jctc.4c00352] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2024]
Abstract
Quantum phase estimation based on qubitization is the state-of-the-art fault-tolerant quantum algorithm for computing ground-state energies in chemical applications. In this context, the 1-norm of the Hamiltonian plays a fundamental role in determining the total number of required iterations and also the overall computational cost. In this work, we introduce the symmetry-compressed double factorization (SCDF) approach, which combines a CDF of the Hamiltonian with the symmetry shift technique, significantly reducing the 1-norm value. The effectiveness of this approach is demonstrated numerically by considering various benchmark systems, including the FeMoco molecule, cytochrome P450, and hydrogen chains of different sizes. To compare the efficiency of SCDF to other methods in absolute terms, we estimate Toffoli gate requirements, which dominate the execution time on fault-tolerant quantum computers. For the systems considered here, SCDF leads to a sizable reduction of the Toffoli gate count in comparison to other variants of DF or even tensor hypercontraction, which is usually regarded as the most efficient approach for qubitization.
Collapse
Affiliation(s)
- Dario Rocca
- QC Ware Corporation, Palo Alto, California 94306, United States
| | | | | | | | | | | | - Matthias Degroote
- Quantum Lab, Boehringer Ingelheim, 55218 Ingelheim am Rhein, Germany
| | - Nikolaj Moll
- Quantum Lab, Boehringer Ingelheim, 55218 Ingelheim am Rhein, Germany
| | | | - Michael Streif
- Quantum Lab, Boehringer Ingelheim, 55218 Ingelheim am Rhein, Germany
| |
Collapse
|
6
|
Takemasa Y, Nozaki K. Hexakispyrazolylethane: New Strategy for Stabilization of Hexaarylethane. Chemistry 2023:e202303575. [PMID: 38095099 DOI: 10.1002/chem.202303575] [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: 10/28/2023] [Indexed: 01/25/2024]
Abstract
Hexakis(4-trimethylsilylpyrazol-1-yl)ethane was synthesized by the oxidative dimerization of tris(4-trimethylsilylpyrazol-1-yl)methane. Single-crystal X-ray structural analysis of hexakis(4-trimethylsilylpyrazol-1-yl)ethane showed that the ethane C-C bond (1.623(4) Å) is shorter than that in hexaphenylethane (1.67(3) Å). In solution, hexakis(4-trimethylsilylpyrazol-1-yl)ethane existed as a single species, contrastive that conventional hexaphenylethanes can keep the central C-C bond only by the aid of additional bridges between the two triarylmethyl units. Theoretical calculations indicated that the tris(pyrazol-1-yl)methyl radical, which is anticipated to be under equilibrium with hexakis(pyrazol-1-yl)ethane, is less stable than trityl radicals due to lack of delocalization of the radicals. Furthermore, introduction of pyrazole groups allowed additional bridging between the two triarylmethyl moieties through metal coordination to the adjacent N atoms: hexakis(4-trimethylsilylpyrazol-1-yl)ethane exhibited unique coordination to three Ag atoms affording a hexaarylethane analog bearing three N-Ag-N bridges.
Collapse
Affiliation(s)
- Yuta Takemasa
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| | - Kyoko Nozaki
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
| |
Collapse
|
7
|
Rock CA, Tschumper GS. Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory. Int J Mol Sci 2023; 24:17480. [PMID: 38139311 PMCID: PMC10744083 DOI: 10.3390/ijms242417480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H2O clusters containing three-five water molecules (Ar(H2O)n=3-5). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body-many-body (2b:Mb) and three-body-many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H2O)4 and three for (H2O)5. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H2O)n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol-1 and by nearly 6 kJ mol-1 for one Ar(H2O)5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm-1 for some hydrogen-bonded OH stretching frequencies.
Collapse
Affiliation(s)
| | - Gregory S. Tschumper
- Department of Chemistry and Biochemistry, University of Mississippi, University, MS 38677-1848, USA
| |
Collapse
|
8
|
Phan Dang CT, Tam NM, Huynh TN, Trung NT. Revisiting conventional noncovalent interactions towards a complete understanding: from tetrel to pnicogen, chalcogen, and halogen bond. RSC Adv 2023; 13:31507-31517. [PMID: 37901266 PMCID: PMC10606978 DOI: 10.1039/d3ra06078k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/23/2023] [Indexed: 10/31/2023] Open
Abstract
Typical noncovalent interactions, including tetrel (TtB), pnicogen (PniB), chalcogen (ChalB), and halogen bonds (HalB), were systematically re-investigated by modeling the N⋯Z interactions (Z = Si, P, S, Cl) between NH3 - as a nucleophilic, and SiF4, PF3, SF2, and ClF - as electrophilic components, employing highly reliable ab initio methods. The characteristics of N⋯Z interactions when Z goes from Si to Cl, were examined through their changes in stability, vibrational spectroscopy, electron density, and natural orbital analyses. The binding energies of these complexes at CCSD(T)/CBS indicate that NH3 tends to hold tightly most with ClF (-34.7 kJ mol-1) and SiF4 (-23.7 kJ mol-1) to form N⋯Cl HalB and N⋯Si TtB, respectively. Remarkably, the interaction energies obtained from various approaches imply that the strength of these noncovalent interactions follows the order: N⋯Si TtB > N⋯Cl HalB > N⋯S ChalB > N⋯P PniB, that differs the order of their corresponding complex stability. The conventional N⋯Z noncovalent interactions are characterized by the local vibrational frequencies of 351, 126, 167, and 261 cm-1 for TtB, PniB, ChalB, and HalB, respectively. The SAPT2+(3)dMP2 calculations demonstrate that the primary force controlling their strength retains the electrostatic term. Accompanied by the stronger strength of N⋯Si TtB and N⋯Cl HalB, the AIM and NBO results state that they are partly covalent in nature with amounts of 18.57% and 27.53%, respectively. Among various analysis approaches, the force constant of the local N⋯Z stretching vibration is shown to be most accurate in describing the noncovalent interactions.
Collapse
Affiliation(s)
- Cam-Tu Phan Dang
- Faculty of Natural Sciences, Duy Tan University Da Nang 550000 Vietnam
- Institute of Research and Development, Duy Tan University Da Nang 550000 Vietnam
| | - Nguyen Minh Tam
- Faculty of Basic Sciences, University of Phan Thiet 225 Nguyen Thong Phan Thiet City Binh Thuan Vietnam
| | - Thanh-Nam Huynh
- Institute of Catalysis Research and Technology, Karlsruhe Institute of Technology Eggenstein-Leopoldshafen 76344 Germany
| | - Nguyen Tien Trung
- Laboratory of Computational Chemistry and Modelling (LCCM), Quy Nhon University Quy Nhon City 590000 Vietnam
| |
Collapse
|
9
|
Jiang Y, Hu Z, Zhong C, Yang Y, Wang XB, Sun Z, Sun H, Liu Z, Peng P. Locking water molecules via ternary O-H⋯O intramolecular hydrogen bonds in perhydroxylated closo-dodecaborate. Phys Chem Chem Phys 2023; 25:25810-25817. [PMID: 37724455 DOI: 10.1039/d3cp03555g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023]
Abstract
A multitude of applications related to perhydroxylated closo-dodecaborate B12(OH)122- in the condensed phase are inseparable from the fundamental mechanisms underlying the high water orientation selectivity based on the base B12(OH)122-. Herein, we directly compare the structural evolution of water clusters, ranging from monomer to hexamer, oriented by functional groups in the bases B12H122-, B12H11OH2- and B12(OH)122- using multiple theoretical methods. A significant revelation is made regarding B12(OH)122-: each additional water molecule is locked into the intramolecular hydrogen bond B-O-H ternary ring in an embedded form. This new pattern of water cluster growth suggests that B-(H-O)⋯H-O interactions prevail over the competition from water-hydrogen bonds (O⋯H-O), distinguishing it from the behavior observed in B12H122- and B12H11OH2- bases, in which competition arises from a mixed competing model involving dihydrogen bonds (B-H⋯H-O), conventional hydrogen bonds (B-(H-O)⋯H-O) and water hydrogen bonds (O⋯H-O). Through aqueous solvation and ab initio molecular dynamics analysis, we further demonstrate the largest water clusters in the first hydrated shell with exceptional thermodynamic stability around B12(OH)122-. These findings provide a solid scientific foundation for the design of boron cluster chemistry incorporating hydroxyl-group-modified borate salts with potential implications for various applications.
Collapse
Affiliation(s)
- Yanrong Jiang
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Cheng Zhong
- College of Chemistry & Molecular Sciences, Wuhan University, Wuhan, Hubei 430072, China
| | - Yan Yang
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, USA
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200241, China.
| | - Zhi Liu
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
| | - Peng Peng
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China.
| |
Collapse
|
10
|
West AML, Dominelli‐Whiteley N, Smolyar IV, Nichol GS, Cockroft SL. Experimental Quantification of Halogen⋅⋅⋅Arene van der Waals Contacts. Angew Chem Int Ed Engl 2023; 62:e202309682. [PMID: 37470309 PMCID: PMC10953438 DOI: 10.1002/anie.202309682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/18/2023] [Accepted: 07/19/2023] [Indexed: 07/21/2023]
Abstract
Crystallographic and computational studies suggest the occurrence of favourable interactions between polarizable arenes and halogen atoms. However, the systematic experimental quantification of halogen⋅⋅⋅arene interactions in solution has been hindered by the large variance in the steric demands of the halogens. Here we have synthesized molecular balances to quantify halogen⋅⋅⋅arene contacts in 17 solvents and solvent mixtures using 1 H NMR spectroscopy. Calculations indicate that favourable halogen⋅⋅⋅arene interactions arise from London dispersion in the gas phase. In contrast, comparison of our experimental measurements with partitioned SAPT0 energies indicate that dispersion is sufficiently attenuated by the solvent that the halogen⋅⋅⋅arene interaction trend was instead aligned with increasing exchange repulsion as the halogen increased in size (ΔGX ⋅⋅⋅Ph =0 to +1.5 kJ mol-1 ). Halogen⋅⋅⋅arene contacts were slightly less disfavoured in solvents with higher solvophobicities and lower polarizabilities, but strikingly, were always less favoured than CH3 ⋅⋅⋅arene contacts (ΔGMe ⋅⋅⋅Ph =0 to -1.4 kJ mol-1 ).
Collapse
Affiliation(s)
- Andrew M. L. West
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Nicholas Dominelli‐Whiteley
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Ivan V. Smolyar
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Gary S. Nichol
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| | - Scott L. Cockroft
- EaStCHEM School of ChemistryUniversity of Edinburgh Joseph Black BuildingDavid Brewster RoadEdinburghEH9 3FJUK
| |
Collapse
|
11
|
Togo T, Tram L, Denton LG, ElHilali-Pollard X, Gu J, Jiang J, Liu C, Zhao Y, Zhao Y, Zheng Y, Zheng Y, Yang J, Fan P, Arkin MR, Härmä H, Sun D, Canan SS, Wheeler SE, Renslo AR. Systematic Study of Heteroarene Stacking Using a Congeneric Set of Molecular Glues for Procaspase-6. J Med Chem 2023; 66:9784-9796. [PMID: 37406165 PMCID: PMC10388292 DOI: 10.1021/acs.jmedchem.3c00590] [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: 04/02/2023] [Indexed: 07/07/2023]
Abstract
Heteroaromatic stacking interactions are important in drug binding, supramolecular chemistry, and materials science, making protein-ligand model systems of these interactions of considerable interest. Here we studied 30 congeneric ligands that each present a distinct heteroarene for stacking between tyrosine residues at the dimer interface of procaspase-6. Complex X-ray crystal structures of 10 analogs showed that stacking geometries were well conserved, while high-accuracy computations showed that heteroarene stacking energy was well correlated with predicted overall ligand binding energies. Empirically determined KD values in this system thus provide a useful measure of heteroarene stacking with tyrosine. Stacking energies are discussed in the context of torsional strain, the number and positioning of heteroatoms, tautomeric state, and coaxial orientation of heteroarene in the stack. Overall, this study provides an extensive data set of empirical and high-level computed binding energies in a versatile new protein-ligand system amenable to studies of other intermolecular interactions.
Collapse
Affiliation(s)
- Takaya Togo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Linh Tram
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Laura G. Denton
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Xochina ElHilali-Pollard
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Jun Gu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jinglei Jiang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Chenglei Liu
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yan Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yanlong Zhao
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yinzhe Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Yunping Zheng
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Jingjing Yang
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Panpan Fan
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Michelle R. Arkin
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| | - Harri Härmä
- Department
of Chemistry, University of Turku, 20500 Turku, Finland
| | - Deqian Sun
- Departments
of Chemistry and Biology, Viva Biotech, Pu Dong New Area, 201203 Shanghai, China
| | - Stacie S. Canan
- Departments of Chemistry
and Structural Biology, Elgia Therapeutics, La Jolla, California 92037, United States
| | - Steven E. Wheeler
- Department
of Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Adam R. Renslo
- Department
of Pharmaceutical Chemistry, University
of California, 600 16th Street, San Francisco, California 94143, United States
| |
Collapse
|
12
|
Yu F, Xu G. Noncovalent Interactions in Hydrated Nitrosonium Ion Clusters Mediated by Hydrogen-Bonded Water Networks. J Phys Chem A 2023. [PMID: 37245158 DOI: 10.1021/acs.jpca.3c01158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
As important species in the D region of the ionosphere, hydrated nitrosonium ion clusters [NO+(H2O)n] are also archetypal and concise models to illustrate effects of different solvent shells. We have investigated noncovalent interactions in NO+(H2O)3 and NO+(H2O)4 isomers with high levels of ab initio and symmetry-adapted perturbation theory (SAPT) methods. On the basis of our computations, the exchange energies become much more repulsive, whereas the induction energies are significantly more attractive for the noncovalent interactions of NO+ with hydrogen-bonded water chains. Combined with analyses of the electron densities for the NO+(H2O)3 and NO+(H2O)4 isomers, we propose that the counteracting effect of the exchange and induction energies could be deemed as an index for the tendency to form the HO-NO covalent bond. Moreover, we have also found that the third-order induction terms are very important to evaluate reasonable charge transfer energies with the SAPT computations.
Collapse
Affiliation(s)
- Feng Yu
- Department of Physics, School of Freshmen, Xi'an Technological University, No. 4 Jinhua North Road, Xi'an 710032, Shaanxi, China
| | - Guohua Xu
- School of Sciences, Xi'an Technological University, No. 4 Jinhua North Road, Xi'an 710032, Shaanxi, China
| |
Collapse
|
13
|
Sohail U, Ullah F, Binti Zainal Arfan NH, Abdul Hamid MHS, Mahmood T, Sheikh NS, Ayub K. Transition Metal Sensing with Nitrogenated Holey Graphene: A First-Principles Investigation. Molecules 2023; 28:molecules28104060. [PMID: 37241800 DOI: 10.3390/molecules28104060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Revised: 04/25/2023] [Accepted: 05/04/2023] [Indexed: 05/28/2023] Open
Abstract
The toxicity of transition metals, including copper(II), manganese(II), iron(II), zinc(II), hexavalent chromium, and cobalt(II), at elevated concentrations presents a significant threat to living organisms. Thus, the development of efficient sensors capable of detecting these metals is of utmost importance. This study explores the utilization of two-dimensional nitrogenated holey graphene (C2N) nanosheet as a sensor for toxic transition metals. The C2N nanosheet's periodic shape and standard pore size render it well suited for adsorbing transition metals. The interaction energies between transition metals and C2N nanosheets were calculated in both gas and solvent phases and were found to primarily result from physisorption, except for manganese and iron which exhibited chemisorption. To assess the interactions, we employed NCI, SAPT0, and QTAIM analyses, as well as FMO and NBO analysis, to examine the electronic properties of the TM@C2N system. Our results indicated that the adsorption of copper and chromium significantly reduced the HOMO-LUMO energy gap of C2N and significantly increased its electrical conductivity, confirming the high sensitivity of C2N towards copper and chromium. The sensitivity test further confirmed the superior sensitivity and selectivity of C2N towards copper. These findings offer valuable insight into the design and development of sensors for the detection of toxic transition metals.
Collapse
Affiliation(s)
- Uroosa Sohail
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Faizan Ullah
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | | | | | - Tariq Mahmood
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department of Chemistry, College of Science, University of Bahrain, Isa Town 32038, Bahrain
| | - Nadeem S Sheikh
- Chemical Sciences, Faculty of Science, Universiti Brunei Darussalam, Jalan Tungku Link, Gadong BE1410, Brunei
| | - Khurshid Ayub
- Department of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| |
Collapse
|
14
|
Bandyopadhyay P, Sadhukhan M. Modeling coarse-grained van der Waals interactions using dipole-coupled anisotropic quantum Drude oscillators. J Comput Chem 2023; 44:1164-1173. [PMID: 36645104 DOI: 10.1002/jcc.27073] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/21/2022] [Accepted: 12/23/2022] [Indexed: 01/17/2023]
Abstract
The Quantum Drude Oscillator (QDO) model is a promising candidate for accurately calculating the van der Waals (vdW) interaction. Anisotropic QDO models have recently been used to represent quantum fluctuations of molecular fragments rather than that of single atoms. While this model promises accurate calculation of vdW energy, there is significant room for improvements, such as incorporating a proper fragmentation method, higher-order dispersion corrections, and so forth. The present work attempts to gauge dipole-dipole interactions' ability without fragmentation. A suitable anisotropic damping function is also introduced to work with anisotropic QDO. This revised model accurately predicts the binding energies of vdW complexes for most of the systems considered. This work indicates the limit of dipole approximation for an anisotropic QDO-based model.
Collapse
Affiliation(s)
| | - Mainak Sadhukhan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| |
Collapse
|
15
|
Michalczyk M, Wojtkowiak K, Panek JJ, Jezierska A, Zierkiewicz W. Static and Dynamical Quantum Studies of CX 3-AlX 2 and CSiX 3-BX 2 (X = F, Cl, Br) Complexes with Hydrocyanic Acid: Unusual Behavior of Strong π-Hole at Triel Center. Int J Mol Sci 2023; 24:ijms24097881. [PMID: 37175586 PMCID: PMC10177972 DOI: 10.3390/ijms24097881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 04/20/2023] [Accepted: 04/23/2023] [Indexed: 05/15/2023] Open
Abstract
The set of TX3-TrX2 (T = C, Si, Ge; Tr = B, Al, Ga; X = F, Cl, Br) molecules offers a rather unique opportunity to study both σ-hole and π-hole dimerization on the tetrel and triel ends, respectively. According to the molecular electrostatic potential (MEP) distribution, the π-hole extrema (acidic sites) were more intense than their σ-hole counterparts. The molecules owning the most (CX3-AlX2) and least (SiX3-BX2) intense π-holes were chosen to evaluate their capacities to attract one and two HCN molecules (Lewis bases). We discovered that the energetic characteristics of π-hole dimers severely conflict with the monomers MEP pattern since the weakest π-hole monomer forms a dimer characterized by interaction energy compared to those created by the monomers with noticeably greater power in the π-hole region. This outcome is due to the deformation of the weakest π-hole donor. Furthermore, the MEP analysis for monomers in the geometry of respective dimers revealed a "residual π-hole" site that was able to drive second ligand attachment, giving rise to the two "unusual trimers" examined further by the NCI and QTAIM analyses. Apart from them, the π-hole/π-hole and σ-hole/π-hole trimers have also been obtained throughout this study and described using energetic and geometric parameters. The SAPT approach revealed details of the bonding in one of the "unusual trimers". Finally, Born-Oppenheimer Molecular Dynamics (BOMD) simulations were carried out to investigate the time evolution of the interatomic distances of the studied complexes as well as their stability.
Collapse
Affiliation(s)
- Mariusz Michalczyk
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Kamil Wojtkowiak
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Jarosław J Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland
| | - Wiktor Zierkiewicz
- Faculty of Chemistry, Wrocław University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| |
Collapse
|
16
|
Yamada Y, Kawao T, Urayoshi S, Nakayama K, Nibu Y. Isomer Stability Dependence of Hydrogen-Bonded Benzoxazole Clusters on Solvent Molecules. J Phys Chem A 2023; 127:2536-2544. [PMID: 36919254 DOI: 10.1021/acs.jpca.3c00811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
Abstract
The structures of hydrogen-bonded benzoxazole clusters with methanol and ammonia, BO-(CH3OH)n (n = 1-3) and BO-(NH3)n (n = 1, 2), in a supersonic jet have been investigated by measuring the S1-S0 electronic spectra and isomer-selected vibrational spectra with the aid of quantum chemical calculations. Similar to BO-(H2O)1, two isomers of BO-(NH3)1 were observed, which form two types of hydrogen bond networks starting from the CH bond at the 2-/7-position to the nitrogen atom of BO (C2HN/C7HN). The relative stability of these isomers strongly depends on solvent molecules. Natural bond orbital analysis reveals that the OH···N hydrogen bond is dominant in BO-(H2O)1 and that intermolecular interaction between the CH group and the nitrogen atom of ammonia, especially C2H···N, is significantly enhanced, resulting in a more stable C2HN isomer. Symmetry-adapted perturbation theory calculations indicate that the dispersion interaction between the methyl group of methanol and π electron cloud on the BO ring is responsible for the extreme stability of the C7HN of BO-(CH3OH)1. Furthermore, using time-dependent density functional theory calculations, the isomer tendency of the electronic transition shifts from the monomer origin is reproduced and it is proposed that the significant blue shift in C2HN is due to the shortened C2H bond length upon electronic excitation.
Collapse
Affiliation(s)
- Yuji Yamada
- Department of Chemistry, Graduate School of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Tomoya Kawao
- Department of Chemistry, Graduate School of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Saeka Urayoshi
- Department of Chemistry, Graduate School of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Kyojun Nakayama
- Department of Chemistry, Graduate School of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| | - Yoshinori Nibu
- Department of Chemistry, Graduate School of Science, Fukuoka University, Jonan-ku, Fukuoka 814-0180, Japan
| |
Collapse
|
17
|
Kojasoy V, Tantillo DJ. Importance of Noncovalent Interactions Involving Sulfur Atoms in Thiopeptide Antibiotics─Glycothiohexide α and Nocathiacin I. J Phys Chem A 2023; 127:2081-2090. [PMID: 36855831 DOI: 10.1021/acs.jpca.2c07600] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Noncovalent interactions involving sulfur atoms play essential roles in protein structure and function by significantly contributing to protein stability, folding, and biological activity. Sulfur is a highly polarizable atom that can participate in many types of noncovalent interactions including hydrogen bonding, sulfur-π interactions, and S-lone pair interactions, but the impact of these sulfur-based interactions on molecular recognition and drug design is still often underappreciated. Here, we examine, using quantum chemical calculations, the roles of sulfur-based noncovalent interactions in complex naturally occurring molecules representative of thiopeptide antibiotics: glycothiohexide α and its close structural analogue nocathiacin I. While donor-acceptor orbital interactions make only very small contributions, electrostatic and dispersion contributions are predicted to be significant in many cases. In pursuit of understanding the magnitudes and nature of these noncovalent interactions, we made potential structural modifications that could significantly expand the chemical space of effective thiopeptide antibiotics.
Collapse
Affiliation(s)
- Volga Kojasoy
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California─Davis, Davis, California 95616, United States
| |
Collapse
|
18
|
The Ultrashort Spike-Ring Interaction in Substituted Iron Maiden Molecules. Molecules 2023; 28:molecules28052244. [PMID: 36903489 PMCID: PMC10004599 DOI: 10.3390/molecules28052244] [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: 02/06/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023] Open
Abstract
The in forms of molecular iron maidens are known for their unique ultrashort interaction between the apical hydrogen atom or its small substituent and the surface of the benzene ring. It is generally believed that this forced ultrashort X⋯π contact is associated with high steric hindrance, which is responsible for specific properties of iron maiden molecules. The main aim of this article is to investigate the influence of significant charge enrichment or depletion of the benzene ring on the characteristics of the ultrashort C-X⋯π contact in iron maiden molecules. For this purpose, three strongly electron-donating (-NH2) or strongly electron-withdrawing (-CN) groups were inserted into the benzene ring of in-[34,10][7]metacyclophane and its halogenated (X = F, Cl, Br) derivatives. It is shown that, despite such extremely electron-donating or electron-accepting properties, the considered iron maiden molecules surprisingly reveal quite high resistance to changes in electronic properties.
Collapse
|
19
|
Jiang Y, Cai Z, Yuan Q, Cao W, Hu Z, Sun H, Wang XB, Sun Z. Highly Structured Water Networks in Microhydrated Dodecaborate Clusters. J Phys Chem Lett 2022; 13:11787-11794. [PMID: 36516831 DOI: 10.1021/acs.jpclett.2c03537] [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] [Indexed: 06/17/2023]
Abstract
We report a combined photoelectron spectroscopy and theoretical investigation of a series of size-selected hydrated closo-dodecaborate clusters B12X122-·nH2O (X = H, F, or I; n = 1-6). Distinct structural arrangements of water clusters from monomer to hexamer can be achieved by using different B12X122- bases, illustrating the evident solute specificity. Because B-H···H-O dihydrogen bonds are stronger than O···H-O hydrogen bonds in water, the added water molecules are arranged in a unified binding mode by forming highly structured water networks manipulated by B12H122-. As a comparison, the hydrated B12F122- clusters display similar water evolution for n values of 1 and 2 but different binding modes for larger clusters, while water networks in B12I122- share similarities with the free water clusters. This finding provides a consistent picture of the structural diversity of hydrogen bonding networks in microhydrated dodecaborates and a molecular-level understanding of microsolvation dynamics in aqueous borate chemistry.
Collapse
Affiliation(s)
- Yanrong Jiang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Center for Transformative Science, ShanghaiTech University, Shanghai 201210, China
| | - Zhaojie Cai
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Qinqin Yuan
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Wenjin Cao
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhubin Hu
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
| | - Haitao Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
- NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Xue-Bin Wang
- Physical Sciences Division, Pacific Northwest National Laboratory, 902 Battelle Boulevard, P.O. Box 999, Richland, Washington 99352, United States
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200241, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| |
Collapse
|
20
|
Mráziková K, Kruse H, Mlýnský V, Auffinger P, Šponer J. Multiscale Modeling of Phosphate···π Contacts in RNA U-Turns Exposes Differences between Quantum-Chemical and AMBER Force Field Descriptions. J Chem Inf Model 2022; 62:6182-6200. [PMID: 36454943 DOI: 10.1021/acs.jcim.2c01064] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Phosphate···π, also called anion···π, contacts occur between nucleobases and anionic phosphate oxygens (OP2) in r(GNRA) and r(UNNN) U-turn motifs (N = A,G,C,U; R = A,G). These contacts were investigated using state-of-the-art quantum-chemical methods (QM) to characterize their physicochemical properties and to serve as a reference to evaluate AMBER force field (AFF) performance. We found that phosphate···π interaction energies calculated with the AFF for dimethyl phosphate···nucleobase model systems are less stabilizing in comparison with double-hybrid DFT and that minimum contact distances are larger for all nucleobases. These distance stretches are also observed in large-scale AFF vs QM/MM computations and classical molecular dynamics (MD) simulations on several r(gcGNRAgc) tetraloop hairpins when compared to experimental data extracted from X-ray/cryo-EM structures (res. ≤ 2.5 Å) using the WebFR3D bioinformatic tool. MD simulations further revealed shifted OP2/nucleobase positions. We propose that discrepancies between the QM and AFF result from a combination of missing polarization in the AFF combined with too large AFF Lennard-Jones (LJ) radii of nucleobase carbon atoms in addition to an exaggerated short-range repulsion of the r-12 LJ repulsive term. We compared these results with earlier data gathered on lone pair···π contacts in CpG Z-steps occurring in r(UNCG) tetraloops. In both instances, charge transfer calculations do not support any significant n → π* donation effects. We also investigated thiophosphate···π contacts that showed reduced stabilizing interaction energies when compared to phosphate···π contacts. Thus, we challenge suggestions that the experimentally observed enhanced thermodynamic stability of phosphorothioated r(GNRA) tetraloops can be explained by larger London dispersion.
Collapse
Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| | - Pascal Auffinger
- Architecture et Réactivité de l'ARN, Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire du CNRS, Strasbourg67084, France
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65Brno, Czech Republic
| |
Collapse
|
21
|
Complexes of carbon dioxide with methanol and its monohalogen-substituted: Beyond the tetrel bond. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.140158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
|
22
|
Luo J, Dai H, Zeng C, Wu D, Cao M. A Theoretical Study of the Halogen Bond between Heteronuclear Halogen and Benzene. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27228078. [PMID: 36432179 PMCID: PMC9692316 DOI: 10.3390/molecules27228078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 11/09/2022] [Accepted: 11/15/2022] [Indexed: 11/22/2022]
Abstract
Halogen bonds play an important role in many fields, such as biological systems, drug design and crystal engineering. In this work, the structural characteristics of the halogen bond between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene were studied using density functional theory. The structures of the complexes between heteronuclear halogen and benzene have Cs symmetry. The interaction energies of the complexes between heteronuclear halogen XD (ClF, BrCl, IBr, ICl, BrF and IF) and benzene range from -27.80 to -37.18 kJ/mol, increasing with the increases in the polarity between the atoms of X and D, and are proportional to the angles of a between the Z axis and the covalent bond of heteronuclear halogen. The electron density (ρ) and corresponding Laplacian (∇2ρ) values indicate that the interaction of the heteronuclear halogen and benzene is a typical long-range weak interaction similar to a hydrogen bond. Independent gradient model analysis suggests that the van der Waals is the main interaction between the complexes of heteronuclear halogen and benzene. Symmetry-adapted perturbation theory analysis suggests that the electrostatic interaction is the dominant part in the complexes of C6H6⋯ClF, C6H6⋯ICl, C6H6⋯BrF and C6H6⋯IF, and the dispersion interaction is the main part in the complexes of C6H6⋯BrCl, C6H6⋯IBr.
Collapse
|
23
|
Tikhonov DS, Scutelnic V, Sharapa DI, Krotova AA, Dmitrieva AV, Obenchain DA, Schnell M. Structures of the (Imidazole)nH+ ... Ar (n=1,2,3) complexes determined from IR spectroscopy and quantum chemical calculations. Struct Chem 2022. [DOI: 10.1007/s11224-022-02053-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
AbstractHere, we present new cryogenic infrared spectra of the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) ions. The data was obtained using helium tagging infrared predissociation spectroscopy. The new results were compared with the data obtained by Gerardi et al. (Chem. Phys. Lett. 501:172–178, 2011) using the same technique but with argon as a tag. Comparison of the two experiments, assisted by theoretical calculations, allowed us to evaluate the preferable attachment positions of argon to the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
frame. Argon attaches to nitrogen-bonded hydrogen in the case of the (Imidazole)H$$^+$$
+
ion, while in (Imidazole)$$_{2}\mathrm{H}^{+}$$
2
H
+
and (Imidazole)$$_{3}\mathrm{H}^{+}$$
3
H
+
the preferred docking sites for the argon are in the center of the complex. This conclusion is supported by analyzing the spectral features attributed to the N–H stretching vibrations. Symmetry adapted perturbation theory (SAPT) analysis of the non-covalent forces between argon and the (Imidazole)$$_{n}\mathrm{H}^{+}$$
n
H
+
(n=1,2,3) frame revealed that this switch of docking preference with increasing complex size is caused by an interplay between induction and dispersion interactions.
Collapse
|
24
|
Ibrahim MA, Saeed RR, Shehata MN, Mohamed EE, Soliman ME, Al-Fahemi JH, El-Mageed HA, Ahmed MN, Shawky AM, Moussa NA. Unexplored σ-hole and π-hole interactions in (X2CY)2 complexes (X = F, Cl; Y = O, S). J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
25
|
Chandra Mallojjala S, Sarkar R, Karugu RW, Manna MS, Ray S, Mukherjee S, Hirschi JS. Mechanism and Origin of Remote Stereocontrol in the Organocatalytic Enantioselective Formal C(sp 2)–H Alkylation Using Nitroalkanes as Alkylating Agents. J Am Chem Soc 2022; 144:17399-17406. [PMID: 36108139 DOI: 10.1021/jacs.2c02941] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Experimental 13C kinetic isotope effects (KIEs) and density functional theory (DFT) calculations are used to evaluate the mechanism and origin of enantioselectivity in the formal C(sp2)-H alkylative desymmetrization of cyclopentene-1,3-diones using nitroalkanes as the alkylating agent. An unusual combination of an inverse (∼0.980) and a normal (∼1.033) KIE is observed on the bond-forming carbon atoms of the cyclopentene-1,3-dione and nitroalkane, respectively. These data provide strong support for a mechanism involving reversible carbon-carbon bond formation followed by rate- and enantioselectivity-determining nitro group elimination. The theoretical free-energy profile and the predicted KIEs indicate that this elimination event occurs via an E1cB pathway. The origin of remote stereocontrol is evaluated by distortion-interaction and SAPT0 analyses of the E1cB transition states leading to both enantiomers.
Collapse
Affiliation(s)
| | - Rahul Sarkar
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Rachael W. Karugu
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| | - Madhu Sudan Manna
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Sayan Ray
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Santanu Mukherjee
- Department of Organic Chemistry, Indian Institute of Science, Bangalore 560012, India
| | - Jennifer S. Hirschi
- Department of Chemistry, Binghamton University, Binghamton, New York 13902, United States
| |
Collapse
|
26
|
Milovanović MR, Stanković IM, Živković JM, Ninković DB, Hall MB, Zarić SD. Water: new aspect of hydrogen bonding in the solid state. IUCRJ 2022; 9:639-647. [PMID: 36071797 PMCID: PMC9438494 DOI: 10.1107/s2052252522006728] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
All water-water contacts in the crystal structures from the Cambridge Structural Database with d OO ≤ 4.0 Å have been found. These contacts were analysed on the basis of their geometries and interaction energies from CCSD(T)/CBS calculations. The results show 6729 attractive water-water contacts, of which 4717 are classical hydrogen bonds (d OH ≤ 3.0 Å and α ≥ 120°) with most being stronger than -3.3 kcal mol-1. Beyond the region of these hydrogen bonds, there is a large number of attractive interactions (2062). The majority are antiparallel dipolar interactions, where the O-H bonds of two water molecules lying in parallel planes are oriented antiparallel to each other. Developing geometric criteria for these antiparallel dipoles (β1, β2 ≥ 160°, 80 ≤ α ≤ 140° and T HOHO > 40°) yielded 1282 attractive contacts. The interaction energies of these antiparallel oriented water molecules are up to -4.7 kcal mol-1, while most of the contacts have interaction energies in the range -0.9 to -2.1 kcal mol-1. This study suggests that the geometric criteria for defining attractive water-water interactions should be broader than the classical hydrogen-bonding criteria, a change that may reveal undiscovered and unappreciated interactions controlling molecular structure and chemistry.
Collapse
Affiliation(s)
- Milan R. Milovanović
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Ivana M. Stanković
- Institute of Chemistry, Technology and Metallurgy, University of Belgrade, Njegoševa 12, Belgrade, 11000 Serbia
| | - Jelena M. Živković
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Dragan B. Ninković
- Innovation Center of the Faculty of Chemistry, Studentski trg 12-16, Belgrade 11000, Serbia
| | - Michael B. Hall
- Department of Chemistry, Texas A&M University, College Station, TX 77843-3255, USA
| | - Snežana D. Zarić
- Faculty of Chemistry, University of Belgrade, Studentski trg 12-16, Belgrade 11000, Serbia
| |
Collapse
|
27
|
Villot C, Ballesteros F, Wang D, Lao KU. Coupled Cluster Benchmarking of Large Noncovalent Complexes in L7 and S12L as Well as the C 60 Dimer, DNA-Ellipticine, and HIV-Indinavir. J Phys Chem A 2022; 126:4326-4341. [PMID: 35766331 DOI: 10.1021/acs.jpca.2c01421] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
In this work, we report the benchmark binding energies of the seven complexes within the L7 data set, six host-guest complexes from the S12L data set, a C60 dimer, the DNA-ellipticine intercalation complex, and the largest system of the study, the HIV-indinavir system, which contained 343 atoms or 139 heavy atoms. The high-quality values reported were obtained via a focal point method that relies on the canonical form of second-order Møller-Plesset theory and the domain-based local pair natural orbital scheme for the coupled cluster with single double and perturbative triple excitations [DLPNO-CCSD(T)] extrapolated to the complete basis set (CBS) limit. The results in this work not only corroborate but also improve upon some previous benchmark values for large noncovalent complexes albeit at a relatively steep cost. Although local CCSD(T) and the largely successful fixed-node diffusion Monte Carlo (FN-DMC) have been shown to generally agree for small- to medium-size systems, a discrepancy in their reported binding energy values arises for large complexes, where the magnitude of the disagreement is a definite cause for concern. For example, the largest deviation in the L7 data set was 2.8 kcal/mol (∼10%) on the low end in C3GC. Such a deviation only grows worse in the S12L set, which showed a difference of up to 10.4 kcal/mol (∼25%) by a conservative estimation in buckycatcher-C60. The DNA-ellipticine complex also generated a disagreement of 4.4 kcal/mol (∼10%) between both state-of-the-art methods. The disagreement between local CCSD(T) and FN-DMC in large noncovalent complexes shows that it is urgently needed to have the canonical CCSD(T), the Monte Carlo CCSD(T), or the full configuration interaction quantum Monte Carlo approaches available to large systems on the hundred-atom scale to solve this dilemma. In addition, the performances of cheaper popular computational methods were assessed for the studied complexes with respect to DLPNO-CCSD(T)/CBS. r2SCAN-3c, B97M-V, and PBE0+D4 work well in large noncovalent complexes in this work, and GFN2-xTB performs well in π-π stacking complexes. B97M-V is the most reliable computationally efficient approach to predicting noncovalent interactions for large complexes, being the only one to have binding errors within the so-called 1 kcal/mol "chemical accuracy". The benchmark interaction energies of these host-guest complexes, molecular materials, and biological systems with electronic and medicinal implications provide crucial reference data for the improvement of current and future lower-cost methods.
Collapse
Affiliation(s)
- Corentin Villot
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Francisco Ballesteros
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Danyang Wang
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284 United States
| |
Collapse
|
28
|
Yu F. Origin of the Microsolvation Effect on the Central Barriers of S N2 Reactions. J Phys Chem A 2022; 126:4342-4348. [PMID: 35785958 DOI: 10.1021/acs.jpca.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We have quantitatively analyzed the microsolvation effect on the central barriers of microsolvated bimolecular nucleophilic substitution (SN2) reactions by means of a two-step energy decomposition procedure. According to the first energy decompositions, an obvious increase in the central barrier for a microsolvated SN2 reaction against its unsolvated counterpart can be mainly ascribed to the fact that the interaction between the solute and the conjunct solvent becomes less attractive from the reactant complex to the transition state. On the basis of the second energy decompositions with symmetry-adapted perturbation theory, this less attractive interaction in the transition state is primarily due to the interplay of the changes in the electrostatic, exchange, and induction components. However, the contribution of the change for the dispersion component is relatively small. A distinct linear correlation has also been observed between the changes of the total interaction energies and those of the corresponding electrostatic components for the microsolvated SN2 reactions studied in this work. Moreover, the two-step energy decomposition procedure employed in this work is expected to be extensively applied to the gas phase reactions mediated by molecules or clusters.
Collapse
Affiliation(s)
- Feng Yu
- Department of Physics, School of Freshmen, Xi'an Technological University, No. 4 Jinhua North Road, Xi'an, Shaanxi 710032, China
| |
Collapse
|
29
|
Sohail U, Ullah F, Mahmood T, Muhammad S, Ayub K. Adsorption of Industrial Gases (CH 4, CO 2, and CO) on Olympicene: A DFT and CCSD(T) Investigation. ACS OMEGA 2022; 7:18852-18860. [PMID: 35694488 PMCID: PMC9178626 DOI: 10.1021/acsomega.2c01796] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 05/05/2022] [Indexed: 05/20/2023]
Abstract
Olympicene C19H12, an organic semiconductor, is investigated as an adsorption material for toxic industrial gas molecules such as CH4, CO2, and CO. A deep insight of complexation of CH4, CO2, and CO with olympicene (analyte@OLY) was obtained by interaction energy, symmetry-adopted perturbation theory (SAPT2+), quantum theory of atoms in molecules (QTAIM), density of states (DOS), noncovalent interaction (NCI), and frontier molecular orbital and natural bond orbital analysis. Domain-based local pair natural orbital coupled cluster theory single-point energy calculations were performed using the cc-pVTZ basis set in combination with corresponding auxiliary cc-pVTZ/JK and cc-pVTZ/C basis sets. For all property calculations of doped olympicene complexes, the ωB97M-V functional was employed. The stability trend for interaction energies is CO2@OLY > CH4@OLY > CO@OLY. QTAIM and NCI analysis confirmed the presence of NCIs, where the dispersion factor (in CH4@OLY) has the highest contribution, as revealed from SAPT2+. The chemical sensitivity of the system was evidenced by the origination of new energy states in DOS spectra. The recovery time for the analyte@OLY complex was calculated at 300 K, and an excellent recovery response was observed. All results evidently indicated weak interactions of the olympicene surface with CH4, CO2, and CO.
Collapse
Affiliation(s)
- Uroosa Sohail
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Faizan Ullah
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
| | - Tariq Mahmood
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- Department
of Chemistry, College of Science, University
of Bahrain, P.O. Box
32038, Barhrain 1051, Bahrain
| | - Shabbir Muhammad
- Department
of Chemistry, College of Science, King Khalid
University, P.O. Box 9004, Abha 61413, Saudi Arabia
| | - Khurshid Ayub
- Department
of Chemistry, COMSATS University Islamabad, Abbottabad Campus, Abbottabad 22060, Pakistan
- . Phone: +92-992-383591. Fax: +92-992-383441
| |
Collapse
|
30
|
External Electric Field Effect on the Strength of σ-Hole Interactions: A Theoretical Perspective in Like⋯Like Carbon-Containing Complexes. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27092963. [PMID: 35566307 PMCID: PMC9104924 DOI: 10.3390/molecules27092963] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/17/2022]
Abstract
For the first time, σ-hole interactions within like⋯like carbon-containing complexes were investigated, in both the absence and presence of the external electric field (EEF). The effects of the directionality and strength of the utilized EEF were thoroughly unveiled in the (F-C-F3)2, (F-C-H3)2, and (H-C-F3)2 complexes. In the absence of the EEF, favorable interaction energies, with negative values, are denoted for the (F-C-F3)2 and (H-C-F3)2 complexes, whereas the (F-C-H3)2 complex exhibits unfavorable interactions. Remarkably, the strength of the applied EEF exhibits a prominent role in turning the repulsive forces within the latter complex into attractive ones. The symmetrical nature of the considered like⋯like carbon-containing complexes eradicated the effect of directionality of the EEF. The quantum theory of atoms in molecules (QTAIM), and the noncovalent interaction (NCI) index, ensured the occurrence of the attractive forces, and also outlined the substantial contributions of the three coplanar atoms to the total strength of the studied complexes. Symmetry-adapted perturbation theory (SAPT) results show the dispersion-driven nature of the interactions.
Collapse
|
31
|
Hill JG, Legon AC. Radial Potential Energy Functions of Linear Halogen-Bonded Complexes YX···ClF (YX = FB, OC, SC, N 2) and the Effects of Substituting X by Second-Row Analogues: Mulliken Inner and Outer Complexes. J Phys Chem A 2022; 126:2511-2521. [PMID: 35426668 PMCID: PMC9097511 DOI: 10.1021/acs.jpca.2c01205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Energies
of linear, halogen-bonded complexes in the isoelectronic
series YX···ClF (YX = FB, OC, or N2) are
calculated at several levels of theory as a function of the intermolecular
distance r(X···Cl) to yield radial
potential energy functions. When YX = OC, a secondary minimum is observed
corresponding to lengthened and shortened distances r(ClF) and r(CCl), respectively, relative to the
primary minimum, suggesting a significant contribution from the Mulliken
inner complex structure [O=C–Cl]+···F–. A conventional weak, halogen-bond complex OC···ClF
occurs at the primary minimum. For YX = FB, the primary minimum corresponds
to the inner complex [F=B–Cl]+···F–, while the outer complex FB···ClF is
at the secondary minimum. The effects on the potential energy function
of systematic substitution of Y and X by second-row congeners and
of reversing the order of X and Y are also investigated. Symmetry-adapted
perturbation theory and natural population analyses are applied to
further understand the nature of the various halogen-bond interactions.
Collapse
Affiliation(s)
- J Grant Hill
- Department of Chemistry, University of Sheffield, Sheffield S3 7HF, U.K
| | - Anthony C Legon
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| |
Collapse
|
32
|
Ibrahim MAA, Moussa NAM, Saad SMA, Ahmed MN, Shawky AM, Soliman MES, Mekhemer GAH, Rady ASSM. σ-Hole and LP-Hole Interactions of Pnicogen···Pnicogen Homodimers under the External Electric Field Effect: A Quantum Mechanical Study. ACS OMEGA 2022; 7:11264-11275. [PMID: 35415328 PMCID: PMC8992284 DOI: 10.1021/acsomega.2c00176] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 03/11/2022] [Indexed: 06/14/2023]
Abstract
σ-Hole and lone-pair (lp)-hole interactions within σ-hole···σ-hole, σ-hole···lp-hole, and lp-hole···lp-hole configurations were comparatively investigated on the pnicogen···pnicogen homodimers (PCl3)2, for the first time, under field-free conditions and the influence of the external electric field (EEF). The electrostatic potential calculations emphasized the impressive versatility of the examined PCl3 monomers to participate in σ-hole and lp-hole pnicogen interactions. Crucially, the sizes of σ-hole and lp-hole were enlarged under the influence of the positively directed EEF and decreased in the case of reverse direction. Interestingly, the energetic quantities unveiled more favorability of the σ-hole···lp-hole configuration of the pnicogen···pnicogen homodimers, with significant negative interaction energies, than σ-hole···σ-hole and lp-hole···lp-hole configurations. Quantum theory of atoms in molecules and noncovalent interaction index analyses were adopted to elucidate the nature and origin of the considered interactions, ensuring their closed shell nature and the occurrence of attractive forces within the studied homodimers. Symmetry-adapted perturbation theory-based energy decomposition analysis alluded to the dispersion force as the main physical component beyond the occurrence of the examined interactions. The obtained findings would be considered as a fundamental underpinning for forthcoming studies pertinent to chemistry, materials science, and crystal engineering.
Collapse
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Sherif M. A. Saad
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Muhammad Naeem Ahmed
- Department
of Chemistry, The University of Azad Jammu
and Kashmir, Muzaffarabad 13100, Pakistan
| | - Ahmed M. Shawky
- Science
and Technology Unit (STU), Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | - Mahmoud E. S. Soliman
- Molecular
Modelling and Drug Design Research Group, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Gamal A. H. Mekhemer
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Al-shimaa S. M. Rady
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| |
Collapse
|
33
|
Wojtkowiak K, Jezierska A, Panek JJ. Revealing Intra- and Intermolecular Interactions Determining Physico-Chemical Features of Selected Quinolone Carboxylic Acid Derivatives. Molecules 2022; 27:2299. [PMID: 35408698 PMCID: PMC9000753 DOI: 10.3390/molecules27072299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Revised: 03/24/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
The intra- and intermolecular interactions of selected quinolone carboxylic acid derivatives were studied in monomers, dimers and crystals. The investigated compounds are well-recognized as medicines or as bases for further studies in drug design. We employed density functional theory (DFT) in its classical formulation to develop gas-phase and solvent reaction field (PCM) models describing geometric, energetic and electronic structure parameters for monomers and dimers. The electronic structure was investigated based on the atoms in molecules (AIM) and natural bond orbital (NBO) theories. Special attention was devoted to the intramolecular hydrogen bonds (HB) present in the investigated compounds. The characterization of energy components was performed using symmetry-adapted perturbation theory (SAPT). Finally, the time-evolution methods of Car-Parrinello molecular dynamics (CPMD) and path integral molecular dynamics (PIMD) were employed to describe the hydrogen bond dynamics as well as the spectroscopic signatures. The vibrational features of the O-H stretching were studied using Fourier transformation of the autocorrelation function of atomic velocity. The inclusion of quantum nuclear effects provided an accurate depiction of the bridged proton delocalization. The CPMD and PIMD simulations were carried out in the gas and crystalline phases. It was found that the polar environment enhances the strength of the intramolecular hydrogen bonds. The SAPT analysis revealed that the dispersive forces are decisive factors in the intermolecular interactions. In the electronic ground state, the proton-transfer phenomena are not favourable. The CPMD results showed generally that the bridged proton is localized at the donor side, with possible proton-sharing events in the solid-phase simulation of stronger hydrogen bridges. However, the PIMD enabled the quantitative estimation of the quantum effects inclusion-the proton position was moved towards the bridge midpoint, but no qualitative changes were detected. It was found that the interatomic distance between the donor and acceptor atoms was shortened and that the bridged proton was strongly delocalized.
Collapse
Affiliation(s)
| | - Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland;
| |
Collapse
|
34
|
Interactions between Artificial Channel Protein, Water Molecules, and Ions Based on Theoretical Approaches. Symmetry (Basel) 2022. [DOI: 10.3390/sym14040691] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Contemporary techniques of molecular modeling allow for rational design of several specific classes of artificial proteins. Transmembrane channels are among these classes. A recent successful synthesis of self-assembling, highly symmetrical 12- or 16-helix channels by David Baker’s group prompted us to study interactions between one of these proteins, TMHC6, and low-molecular-weight components of the environment: water molecules and ions. To examine protein stability in a polar environment, molecular dynamics (MD) with classical force fields of the AMBER family was employed. Further characteristics of the chosen interactions were obtained using interaction energy calculations with usage of partially polarizable GFN-FF force field of Spicher and Grimme, symmetry-adapted perturbation theory (SAPT) and atoms in molecules (AIM) approaches for models of residues from the channel entry, crucial for interactions with water molecules and ions. The comparison of the interaction energy values between the gas phase and solvent reaction field gives the quantitative estimation of the strength of the interactions. The energy decomposition via the SAPT method showed that the electrostatics forces play a dominant role in the substructure stabilization. An application of the AIM theory enabled a description of the intermolecular hydrogen bonds and other noncovalent interactions.
Collapse
|
35
|
Pocheć M, Krupka KM, Panek JJ, Orzechowski K, Jezierska A. Intermolecular Interactions and Spectroscopic Signatures of the Hydrogen-Bonded System-n-Octanol in Experimental and Theoretical Studies. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27041225. [PMID: 35209010 PMCID: PMC8878718 DOI: 10.3390/molecules27041225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Revised: 02/06/2022] [Accepted: 02/09/2022] [Indexed: 11/29/2022]
Abstract
n-Octanol is the object of experimental and theoretical study of spectroscopic signatures and intermolecular interactions. The FTIR measurements were carried out at 293 K for n-octanol and its deuterated form. Special attention was paid to the vibrational features associated with the O-H stretching and the isotope effect. Density Functional Theory (DFT) in its classical formulations was applied to develop static models describing intermolecular hydrogen bond (HB) and isotope effect in the gas phase and using solvent reaction field reproduced by Polarizable Continuum Model (PCM). The Atoms in Molecules (AIM) theory enabled electronic structure and molecular topology study. The Symmetry-Adapted Perturbation Theory (SAPT) was used for energy decomposition in the dimers of n-octanol. Finally, time-evolution methods, namely classical molecular dynamics (MD) and Car-Parrinello Molecular Dynamics (CPMD) were employed to shed light onto dynamical nature of liquid n-octanol with emphasis put on metric and vibrational features. As a reference, CPMD gas phase results were applied. Nuclear quantum effects were included using Path Integral Molecular Dynamics (PIMD) and a posteriori method by solving vibrational Schrödinger equation. The latter applied procedure allowed to study the deuterium isotope effect.
Collapse
|
36
|
Jezierska A, Panek JJ, Błaziak K, Raczyński K, Koll A. Exploring Intra- and Intermolecular Interactions in Selected N-Oxides-The Role of Hydrogen Bonds. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27030792. [PMID: 35164056 PMCID: PMC8846293 DOI: 10.3390/molecules27030792] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Revised: 01/20/2022] [Accepted: 01/21/2022] [Indexed: 11/30/2022]
Abstract
Intra- and intermolecular interactions have been explored in selected N-oxide derivatives: 2-(N,N-dimethylamino-N-oxymethyl)-4,6-dimethylphenyl (1) and 5,5’-dibromo-3-diethylaminomethyl-2,2’-biphenol N-oxide (2). Both compounds possess intramolecular hydrogen bonding, which is classified as moderate in 1 and strong in 2, and resonance-assisted in both cases. Density Functional Theory (DFT) in its classical formulation as well as Time-Dependent extension (TD-DFT) were employed to study proton transfer phenomena. The simulations were performed in the gas phase and with implicit and explicit solvation models. The obtained structures of the studied N-oxides were compared with experimental data available. The proton reaction path was investigated using scan with an optimization method, and water molecule reorientation in the monohydrate of 1 was found upon the proton scan progress. It was found that spontaneous proton transfer phenomenon cannot occur in the electronic ground state of the compound 1. An opposite situation was noticed for the compound 2. The changes of nucleophilicity and electrophilicity upon the bridged proton migration were analyzed on the basis of Fukui functions in the case of 1. The interaction energy decomposition of dimers and microsolvation models was investigated using Symmetry-Adapted Perturbation Theory (SAPT). The simulations were performed in both phases to introduce polar environment influence on the interaction energies. The SAPT study showed rather minor role of induction in the formation of homodimers. However, it is worth noticing that the same induction term is responsible for the preference of water molecules’ interaction with N-oxide hydrogen bond acceptor atoms in the microsolvation study. The Natural Bond Orbital (NBO) analysis was performed for the complexes with water to investigate the charge flow upon the polar environment introduction. Finally, the TD-DFT was applied for isolated molecules as well as for microsolvation models showing that the presence of solvent affects excited states, especially when the N-oxide acceptor atom is microsolvated.
Collapse
Affiliation(s)
- Aneta Jezierska
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
- Correspondence: ; Tel.: +48-71-3757-224; Fax: +48-71-3282-348
| | - Jarosław J. Panek
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Kacper Błaziak
- Faculty of Chemistry, University of Warsaw, ul. Pasteura 1, 01-224 Warsaw, Poland;
- Biological and Chemical Research Center, University of Warsaw, Żwirki i Wigury 101, 01-224 Warsaw, Poland
| | - Kamil Raczyński
- Faculty of Chemistry, University of Wrocław, ul. F. Joliot-Curie 14, 50-383 Wrocław, Poland; (J.J.P.); (K.R.)
| | - Aleksander Koll
- Non-Public Medical School in Wrocław, ul. Nowowiejska 69, 50-340 Wrocław, Poland;
| |
Collapse
|
37
|
Ibrahim MAA, Shehata MNI, Soliman MES, Moustafa MF, El-Mageed HRA, Moussa NAM. Unusual chalcogen⋯chalcogen interactions in like⋯like and unlike YCY⋯YCY complexes (Y = O, S, and Se). Phys Chem Chem Phys 2022; 24:3386-3399. [PMID: 35072679 DOI: 10.1039/d1cp02706a] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chalcogen⋯chalcogen interactions were investigated within four types of like⋯like and unlike YCY⋯YCY complexes (where Y = O, S, or Se). A plethora of quantum mechanical calculations, including molecular electrostatic potential (MEP), surface electrostatic potential extrema, point-of-charge (PoC), quantum theory of atoms in molecules (QTAIM), noncovalent interaction (NCI), and symmetry-adapted perturbation theory-based energy decomposition analysis (SAPT-EDA) calculations, were executed. The energetic findings revealed a preferential tendency of the studied chalcogen-bearing molecules to engage in type I, II, III, or IV chalcogen⋯chalcogen interactions. Notably, the selenium-bearing molecules exhibited the most potent ability to favorably participate in all the explored chalcogen⋯chalcogen interactions. Among like⋯like complexes, type IV interactions showed the most favorable negative binding energies, whereas type III interactions exhibited the weakest binding energies. Unexpectedly, oxygen-containing complexes within type IV interactions showed an alien pattern of binding energies that decreased along with an increase in the chalcogen atomic size level. QTAIM analysis provided a solo BCP, via chalcogen⋯chalcogen interactions, with no clues as to any secondary ones. SAPT-EDA outlined the domination of the explored interactions by the dispersion forces and indicated the pivotal shares of the electrostatic forces, except type III σ-hole⋯σ-hole and di-σ-hole interactions. These observations demonstrate in better detail all the types of chalcogen⋯chalcogen interactions, providing persuasive reasons for their more intensive use in versatile fields related to materials science and drug design.
Collapse
Affiliation(s)
- Mahmoud A A Ibrahim
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
| | - Mohammed N I Shehata
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
| | - Mahmoud E S Soliman
- Molecular Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Mahmoud F Moustafa
- Department of Biology, College of Science, King Khalid University, Abha 9004, Saudi Arabia.,Department of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - H R Abd El-Mageed
- Micro-Analysis, Environmental Research and Community Affairs Center (MAESC), Faculty of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Nayra A M Moussa
- Computational Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt.
| |
Collapse
|
38
|
Tulsiyan KD, Jena S, Dutta J, Biswal HS. Hydrogen Bonding with Polonium. Phys Chem Chem Phys 2022; 24:17185-17194. [DOI: 10.1039/d2cp01852g] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bonding (H-bonding) with heavier chalcogens such as polonium and tellurium is almost unexplored owing to their lower electronegativities, providing us an opportunity to delve into the uncharted territory of...
Collapse
|
39
|
Řezáč J. Non-Covalent Interactions Atlas Benchmark Data Sets 5: London Dispersion in an Extended Chemical Space. Phys Chem Chem Phys 2022; 24:14780-14793. [DOI: 10.1039/d2cp01602h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The Non-Covalent Interactions Atlas (www.nciatlas.org) has been extended with two data sets of benchmark interaction energies in complexes dominated by London dispersion. The D1200 data set of equilibrium geometries provides...
Collapse
|
40
|
Rostkowski M, Schürner HKV, Sowińska A, Vasquez L, Przydacz M, Elsner M, Dybala-Defratyka A. Isotope Effects on the Vaporization of Organic Compounds from an Aqueous Solution-Insight from Experiment and Computations. J Phys Chem B 2021; 125:13868-13885. [PMID: 34908428 PMCID: PMC8724799 DOI: 10.1021/acs.jpcb.1c05574] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
An isotope fractionation
analysis of organic groundwater pollutants
can assess the remediation at contaminated sites yet needs to consider
physical processes as potentially confounding factors. This study
explores the predictability of water–air partitioning isotope
effects from experiments and computational predictions for benzene
and trimethylamine (both H-bond acceptors) as well as chloroform (H-bond
donor). A small, but significant, isotope fractionation of different
direction and magnitude was measured with ε = −0.12‰
± 0.07‰ (benzene), εC = 0.49‰
± 0.23‰ (triethylamine), and εH = 1.79‰
± 0.54‰ (chloroform) demonstrating that effects do not
correlate with expected hydrogen-bond functionalities. Computations
revealed that the overall isotope effect arises from contributions
of different nature and extent: a weakening of intramolecular vibrations
in the condensed phase plus additional vibrational modes from a complexation
with surrounding water molecules. Subtle changes in benzene contrast
with a stronger coupling between intra- and intermolecular modes in
the chloroform–water system and a very local vibrational response
with few atoms involved in a specific mode of triethylamine. An energy
decomposition analysis revealed that each system was affected differently
by electrostatics and dispersion, where dispersion was dominant for
benzene and electrostatics dominated for chloroform and triethylamine.
Interestingly, overall stabilization patterns in all studied systems
originated from contributions of dispersion rather than other energy
terms.
Collapse
Affiliation(s)
- Michał Rostkowski
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Heide K V Schürner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Agata Sowińska
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Luis Vasquez
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Martyna Przydacz
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| | - Martin Elsner
- Chair of Analytical Chemistry and Water Chemistry, Technical University of Munich, Elisabeth-Winterhalter-Weg 6, 81377 Munich, Germany
| | - Agnieszka Dybala-Defratyka
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz, Poland
| |
Collapse
|
41
|
Three types of noncovalent interactions studied between pyrazine and XF. J Mol Model 2021; 28:15. [PMID: 34961885 DOI: 10.1007/s00894-021-05012-8] [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: 10/15/2021] [Accepted: 12/15/2021] [Indexed: 10/19/2022]
Abstract
Three types noncovalent interactions (type I, II and III) between pyrazine (C4H4N2) and XF (X = F, Cl, Br, and I) have been discovered at the MP2/aug-cc-pVTZ level. TypeI is σ-hole interaction between the positive site on the halogen X of XF and the negative site on one of the pyrazine nitrogens. Type II is counterintuitive σ-hole interaction driven by polarization between the positive site on the halogen X of XF and a portion of the pyrazine ring. Type III is an interaction between the lateral regions of the halogen X of XF and the position of the pyrazine ring. Through comparing the calculated interaction energy, we can know that the type II and type III interactions are weaker than the corresponding type I interactions, and type III interactions are weaker than the corresponding type II interactions in C4H4N2-XF complexes. SAPT analysis shows that the electrostatic energy are the major source of the attraction for the type I (σ-hole) interactions while the type III interactions are mainly dispersion energy. For the type II (counterintuitive σ-hole) interactions in C4H4N2-XF (X = F and Cl) complexes, electrostatic energy are the major source of the attraction, while in C4H4N2-XF (X = Br and I) complexes, the electrostatic term, induction and dispersion play equally important role in the total attractive interaction. NBO analysis, AIM theory, and conceptual DFT are also being utilized.
Collapse
|
42
|
Robalo JR, Mendes de Oliveira D, Ben-Amotz D, Vila Verde A. Influence of Methylene Fluorination and Chain Length on the Hydration Shell Structure and Thermodynamics of Linear Diols. J Phys Chem B 2021; 125:13552-13564. [PMID: 34875166 DOI: 10.1021/acs.jpcb.1c08601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interplay between the local hydration shell structure, the length of hydrophobic solutes, and their identity (perfluorinated or not) remains poorly understood. We address this issue by combining Raman-multivariate curve resolution (Raman-MCR) spectroscopy, simulation, and quantum-mechanical calculations to quantify the thermodynamics and the first principle interactions behind the formation of defects in the hydration shell of alkyl-diol and perfluoroalkyl-diol chains. The hydration shell of the fluorinated diols contains substantially more defects than that of the nonfluorinated diols; these defects are water hydroxy groups that do not donate hydrogen bonds and which either point to the solute (radial-dangling OH) or not (nonradial-dangling OH). The number of radial-dangling OH defects per carbon decreases for longer chains and toward the interior of the fluorinated diols, mainly due to less favorable electrostatics and exchange interactions; nonradial-dangling OH defects per carbon increase with chain length. In contrast, the hydration shell of the nonfluorinated diols only contains radial-dangling defects, which become more abundant toward the center of the chain and for larger chains, predominantly because of more favorable dispersion interactions. These results have implications for how the folding of macromolecules, ligand binding to biomacromolecules, and chemical reactions at water-oil interfaces could be modified through the introduction of fluorinated groups or solvents.
Collapse
Affiliation(s)
- João R Robalo
- Department of Theory & Bio-systems, Max Planck Institute for Colloids and Interfaces, Science Park, Potsdam 14476, Germany
| | | | - Dor Ben-Amotz
- Purdue University, Department of Chemistry, West Lafayette, Indiana 47907, United States
| | - Ana Vila Verde
- University of Duisburg-Essen, Faculty of Physics, Lotharstrasse 1, 47057 Duisburg, Germany
| |
Collapse
|
43
|
Camiruaga A, Usabiaga I, Calabrese C, Lamas I, Basterretxea FJ, Fernández JA. Exploring the Influence of Intermolecular Interactions in Prebiotic Chemistry Using Laser Spectroscopy and Calculations. Chemistry 2021; 28:e202103636. [PMID: 34854511 PMCID: PMC9299682 DOI: 10.1002/chem.202103636] [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: 10/07/2021] [Indexed: 11/09/2022]
Abstract
One of the most fascinating questions in chemistry is why nature chose CGAT as the alphabet of life. Very likely, such selection was the result of multiple factors and a long period of refinement. Here, we explore how the intermolecular interactions influenced such process, by characterizing the formation of dimers between adenine, theobromine and 4-aminopyrimidine. Using a combination of mass-resolved excitation spectroscopy and DFT calculations, we determined the structure of adenine-theobromine and 4-aminopyrimidine-theobromine dimers. The binding energy of these dimers is very close to the canonical adenine-thymine nucleobases. Likewise, the dimers are able to adopt Watson-Crick conformations. These findings seem to indicate that there were many options available to build the first versions of the informational polymers, which also had to compete with other molecules, such as 4-aminopyrimidine, which does not have a valid attaching point for a saccharide. For some reason, nature did not select the most strongly-bonded partners or if it did, such proto-bases were later replaced by the nowadays canonical CGAT.
Collapse
Affiliation(s)
- Ander Camiruaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Imanol Usabiaga
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Camilla Calabrese
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain.,Instituto Biofisika (UPV/EHU-CSIC), University of the Basque Country (UPV/EHU), Barrio Sarriena S/N, Leioa, 48940, Spain
| | - Iker Lamas
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - Francisco J Basterretxea
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| | - José A Fernández
- Department of Physical Chemistry, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), Barrio Sarriena, S/N, Leioa, 48940, Spain
| |
Collapse
|
44
|
Mráziková K, Šponer J, Mlýnský V, Auffinger P, Kruse H. Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose···Nucleobase Lone-Pair···π Contacts in Nucleic Acids. J Chem Inf Model 2021; 61:5644-5657. [PMID: 34738826 DOI: 10.1021/acs.jcim.1c01047] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The lone-pair···π (lp···π) (deoxy)ribose···nucleobase stacking is a recurring interaction in Z-DNA and RNAs that is characterized by sub-van der Waals lp···π contacts (<3.0 Å). It is a part of the structural signature of CpG Z-step motifs in Z-DNA and r(UNCG) tetraloops that are known to behave poorly in molecular dynamics (MD) simulations. Although the exact origin of the MD simulation issues remains unclear, a significant part of the problem might be due to an imbalanced description of nonbonded interactions, including the characteristic lp···π stacking. To gain insights into the links between lp···π stacking and MD, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the nonbonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, and U). Among other differences, we found that the AFF overestimates the DHDF-D3 lp···π distances by ∼0.1-0.2 Å, while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule polarizabilities and symmetry-adapted perturbation theory analysis, we inferred that the DHDF-D3 versus AFF differences partly originate in identical nucleobase carbon atom Lennard-Jones (LJ) parameters despite the presence/absence of connected electron-withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp···π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.
Collapse
Affiliation(s)
- Klaudia Mráziková
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Kamenice 5, 625 00 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Vojtěch Mlýnský
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Czech Advanced Technology and Research Institute (CATRIN), Palacky University Olomouc, Šlechtitelů 241/27, 783 71 Olomouc-Holice, Czech Republic
| | - Pascal Auffinger
- Architecture and Reactivity of RNA, University of Strasbourg, Institute of Molecular and Cellular Biology of the CNRS, 67084 Strasbourg, France
| | - Holger Kruse
- Institute of Biophysics of the Czech Academy of Sciences, Královopolská 135, 612 65 Brno, Czech Republic
| |
Collapse
|
45
|
Ibrahim MAA, Mohamed YAM, Abuelliel HAA, Rady ASM, Soliman MES, Ahmed MN, Mohamed LA, Moussa NAM. σ‐Hole Interactions of Tetrahedral Group IV–VIII Lewis Acid Centers with Lewis Bases: A Comparative Study. ChemistrySelect 2021. [DOI: 10.1002/slct.202103092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| | - Yasmeen A. M. Mohamed
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| | - Hassan A. A. Abuelliel
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| | - Al‐shimaa S. M. Rady
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| | - Mahmoud E. S. Soliman
- Molecular Bio-computation and Drug Design Lab School of Health Sciences University of KwaZulu-Natal Westville, Durban 4000 South Africa
| | - Muhammad Naeem Ahmed
- Department of Chemistry The University of Azad Jammu and Kashmir Muzaffarabad 13100 Pakistan
| | - Lamiaa A. Mohamed
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| | - Nayra A. M. Moussa
- Computational Chemistry Laboratory Chemistry Department Faculty of Science Minia University Minia 61519 Egypt
| |
Collapse
|
46
|
Sparrow ZM, Ernst BG, Joo PT, Lao KU, DiStasio RA. NENCI-2021. I. A large benchmark database of non-equilibrium non-covalent interactions emphasizing close intermolecular contacts. J Chem Phys 2021; 155:184303. [PMID: 34773949 DOI: 10.1063/5.0068862] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present NENCI-2021, a benchmark database of ∼8000 Non-Equilibirum Non-Covalent Interaction energies for a large and diverse selection of intermolecular complexes of biological and chemical relevance. To meet the growing demand for large and high-quality quantum mechanical data in the chemical sciences, NENCI-2021 starts with the 101 molecular dimers in the widely used S66 and S101 databases and extends the scope of these works by (i) including 40 cation-π and anion-π complexes, a fundamentally important class of non-covalent interactions that are found throughout nature and pose a substantial challenge to theory, and (ii) systematically sampling all 141 intermolecular potential energy surfaces (PESs) by simultaneously varying the intermolecular distance and intermolecular angle in each dimer. Designed with an emphasis on close contacts, the complexes in NENCI-2021 were generated by sampling seven intermolecular distances along each PES (ranging from 0.7× to 1.1× the equilibrium separation) and nine intermolecular angles per distance (five for each ion-π complex), yielding an extensive database of 7763 benchmark intermolecular interaction energies (Eint) obtained at the coupled-cluster with singles, doubles, and perturbative triples/complete basis set [CCSD(T)/CBS] level of theory. The Eint values in NENCI-2021 span a total of 225.3 kcal/mol, ranging from -38.5 to +186.8 kcal/mol, with a mean (median) Eint value of -1.06 kcal/mol (-2.39 kcal/mol). In addition, a wide range of intermolecular atom-pair distances are also present in NENCI-2021, where close intermolecular contacts involving atoms that are located within the so-called van der Waals envelope are prevalent-these interactions, in particular, pose an enormous challenge for molecular modeling and are observed in many important chemical and biological systems. A detailed symmetry-adapted perturbation theory (SAPT)-based energy decomposition analysis also confirms the diverse and comprehensive nature of the intermolecular binding motifs present in NENCI-2021, which now includes a significant number of primarily induction-bound dimers (e.g., cation-π complexes). NENCI-2021 thus spans all regions of the SAPT ternary diagram, thereby warranting a new four-category classification scheme that includes complexes primarily bound by electrostatics (3499), induction (700), dispersion (1372), or mixtures thereof (2192). A critical error analysis performed on a representative set of intermolecular complexes in NENCI-2021 demonstrates that the Eint values provided herein have an average error of ±0.1 kcal/mol, even for complexes with strongly repulsive Eint values, and maximum errors of ±0.2-0.3 kcal/mol (i.e., ∼±1.0 kJ/mol) for the most challenging cases. For these reasons, we expect that NENCI-2021 will play an important role in the testing, training, and development of next-generation classical and polarizable force fields, density functional theory approximations, wavefunction theory methods, and machine learning based intra- and inter-molecular potentials.
Collapse
Affiliation(s)
- Zachary M Sparrow
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Brian G Ernst
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Paul T Joo
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Ka Un Lao
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| | - Robert A DiStasio
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, USA
| |
Collapse
|
47
|
Ibrahim MAA, Kamel AAK, Soliman MES, Moustafa MF, El-Mageed HRA, Taha F, Mohamed LA, Moussa NAM. Effect of External Electric Field on Tetrel Bonding Interactions in (FTF 3···FH) Complexes (T = C, Si, Ge, and Sn). ACS OMEGA 2021; 6:25476-25485. [PMID: 34632205 PMCID: PMC8495869 DOI: 10.1021/acsomega.1c03461] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 09/14/2021] [Indexed: 05/13/2023]
Abstract
A quantum chemical study was accomplished on the σ-hole interactions of the barely explored group IV elements, for the first time, in the absence and presence of the positively and negatively directed external electric field (EEF). The analyses of molecular electrostatic potential addressed the occurrence of the σ-hole on all the inspected tetrel atoms, confirming their salient versatility to engage in σ-hole interactions. MP2 energetic findings disclosed the occurrence of favorable σ-hole interactions within the tetrel bonding complexes. The tetrel bonding interactions became stronger in the order of C < Si < Ge < Sn for F-T-F3···FH complexes with the largest interaction energy amounting to -19.43 kcal/mol for the optimized F-Sn-F3···FH complex under the influence of +0.020 au EEF. The interaction energy conspicuously evolved by boosting the magnitude of the positively directed EEF value and declining the negatively directed EEF one. The decomposition analysis for the interaction energies was also executed in terms of symmetry-adapted perturbation theory, illuminating the dominant electrostatic contribution to all the studied complexes' interactions except carbon-based interactions controlled by dispersion forces. The outcomes that emerged from the current work reported significantly how the direction and strength of the EEF affect the tetrel-bonding interactions, leading to further improvements in the forthcoming studies of supramolecular chemistry and materials science.
Collapse
Affiliation(s)
- Mahmoud A. A. Ibrahim
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Afnan A. K. Kamel
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Mahmoud E. S. Soliman
- Molecular
Bio-computation and Drug Design Lab, School of Health Sciences, University of KwaZulu-Natal, Westville, Durban 4000, South Africa
| | - Mahmoud F. Moustafa
- Department
of Biology, College of Science, King Khalid
University, Abha 9004, Saudi Arabia
- Department
of Botany & Microbiology, Faculty of Science, South Valley University, Qena 83523, Egypt
| | - H. R. Abd El-Mageed
- Micro-Analysis,
Environmental Research and Community Affairs Center (MAESC), Faculty
of Science, Beni-Suef University, Beni-Suef 62511, Egypt
| | - Fouad Taha
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Lamiaa A. Mohamed
- Chemistry
Department, Faculty of Science, Minia University, Minia 61519, Egypt
| | - Nayra A. M. Moussa
- Computational
Chemistry Laboratory, Chemistry Department, Faculty of Science, Minia University, Minia 61519, Egypt
| |
Collapse
|
48
|
Naphthazarin Derivatives in the Light of Intra- and Intermolecular Forces. Molecules 2021; 26:molecules26185642. [PMID: 34577113 PMCID: PMC8468954 DOI: 10.3390/molecules26185642] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 09/04/2021] [Accepted: 09/14/2021] [Indexed: 11/17/2022] Open
Abstract
Our long-term investigations have been devoted the characterization of intramolecular hydrogen bonds in cyclic compounds. Our previous work covers naphthazarin, the parent compound of two systems discussed in the current work: 2,3-dimethylnaphthazarin (1) and 2,3-dimethoxy-6-methylnaphthazarin (2). Intramolecular hydrogen bonds and substituent effects in these compounds were analyzed on the basis of Density Functional Theory (DFT), Møller-Plesset second-order perturbation theory (MP2), Coupled Clusters with Singles and Doubles (CCSD) and Car-Parrinello Molecular Dynamics (CPMD). The simulations were carried out in the gas and crystalline phases. The nuclear quantum effects were incorporated a posteriori using the snapshots taken from ab initio trajectories. Further, they were used to solve a vibrational Schrödinger equation. The proton reaction path was studied using B3LYP, ωB97XD and PBE functionals with a 6-311++G(2d,2p) basis set. Two energy minima (deep and shallow) were found, indicating that the proton transfer phenomena could occur in the electronic ground state. Next, the electronic structure and topology were examined in the molecular and proton transferred (PT) forms. The Atoms In Molecules (AIM) theory was employed for this purpose. It was found that the hydrogen bond is stronger in the proton transferred (PT) forms. In order to estimate the dimers' stabilization and forces responsible for it, the Symmetry-Adapted Perturbation Theory (SAPT) was applied. The energy decomposition revealed that dispersion is the primary factor stabilizing the dimeric forms and crystal structure of both compounds. The CPMD results showed that the proton transfer phenomena occurred in both studied compounds, as well as in both phases. In the case of compound 2, the proton transfer events are more frequent in the solid state, indicating an influence of the environmental effects on the bridged proton dynamics. Finally, the vibrational signatures were computed for both compounds using the CPMD trajectories. The Fourier transformation of the autocorrelation function of atomic velocity was applied to obtain the power spectra. The IR spectra show very broad absorption regions between 700 cm-1-1700 cm-1 and 2300 cm-1-3400 cm-1 in the gas phase and 600 cm-1-1800 cm-1 and 2200 cm-1-3400 cm-1 in the solid state for compound 1. The absorption regions for compound 2 were found as follows: 700 cm-1-1700 cm-1 and 2300 cm-1-3300 cm-1 for the gas phase and one broad absorption region in the solid state between 700 cm-1 and 3100 cm-1. The obtained spectroscopic features confirmed a strong mobility of the bridged protons. The inclusion of nuclear quantum effects showed a stronger delocalization of the bridged protons.
Collapse
|
49
|
Schaefer AJ, Ingman VM, Wheeler SE. SEQCROW: A ChimeraX bundle to facilitate quantum chemical applications to complex molecular systems. J Comput Chem 2021; 42:1750-1754. [PMID: 34109660 DOI: 10.1002/jcc.26700] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/21/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022]
Abstract
We describe a bundle for UCSF ChimeraX called SEQCROW that provides advanced structure editing capabilities and quantum chemistry utilities designed for complex organic and organometallic compounds. SEQCROW includes graphical presets and bond editing tools that facilitate the generation of publication-quality molecular structure figures while also allowing users to build molecular structures quickly and efficiently by mapping new ligands onto existing organometallic complexes as well as adding rings and substituents. Other capabilities include the ability to visualize vibrational modes and simulated IR spectra, to compute and visualize molecular descriptors including percent buried volume, ligand cone angles, and Sterimol parameters, to process thermochemical corrections from quantum mechanical computations, to generate input files for ORCA, Psi4, and Gaussian, and to run and manage computational jobs.
Collapse
Affiliation(s)
| | - Victoria M Ingman
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| | - Steven E Wheeler
- Department of Chemistry, University of Georgia, Athens, Georgia, USA
| |
Collapse
|
50
|
Jing X, Zeng Y, Zhang X, Meng L, Li X. Competition and conversion between pnicogen bonds and hydrogen bonds involving prototype organophosphorus compounds. Phys Chem Chem Phys 2021; 23:18794-18805. [PMID: 34612418 DOI: 10.1039/d1cp00474c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ab initio calculations have been performed to investigate the competition and conversion between the pnicogen bonds and hydrogen bonds in complexes containing prototype organophosphorus compounds RPO2 (R = CH3 and CH3O). The competition between the pnicogen bonds and hydrogen bonds is controlled by the magnitude of Vs,min and Vs,max in the prototype organophosphorus compounds. Monomeric methyl metaphosphate (CH3OPO2), with more positive π-holes, is more likely to form pnicogen bonds with different electron donors, such as NH3, H2O, HNC and HCCH. Methoxyphosphinidene oxide (trans- and cis-CH3OPO) is inclined to form hydrogen bonds with H2O, HNC and HCCH. Most of the pnicogen bonds have covalent or partially covalent character, while most of the hydrogen bonds exhibit the noncovalent characteristics of weak interactions. The mechanisms of three typical conversions between the pnicogen bond and the hydrogen bond have been investigated and the breakage and formation of the bonds along the reaction pathways have been analyzed using topological analysis of electron density. For the three studied conversion processes, the transformation between the hydrogen-bonded complex and pnicogen-bonded complex is achieved readily through several T-shape structure transition states.
Collapse
Affiliation(s)
- Xinyue Jing
- College of Chemistry and Materials Science, Hebei Normal University, Shijiazhuang, 050024, P. R. China.
| | | | | | | | | |
Collapse
|