1
|
Tu NTP, Williamson S, Johnson ER, Rowley CN. Modeling Intermolecular Interactions with Exchange-Hole Dipole Moment Dispersion Corrections to Neural Network Potentials. J Phys Chem B 2024. [PMID: 39166778 DOI: 10.1021/acs.jpcb.4c02882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Neural network potentials (NNPs) are an innovative approach for calculating the potential energy and forces of a chemical system. In principle, these methods are capable of modeling large systems with an accuracy approaching that of a high-level ab initio calculation, but with a much smaller computational cost. Due to their training to density-functional theory (DFT) data and neglect of long-range interactions, some classes of NNPs require an additional term to include London dispersion physics. In this Perspective, we discuss the requirements for a dispersion model for use with an NNP, focusing on the MLXDM (Machine Learned eXchange-Hole Dipole Moment) model developed by our groups. This model is based on the DFT-based XDM dispersion correction, which calculates interatomic dispersion coefficients in terms of atomic moments and polarizabilities, both of which can be approximated effectively using neural networks.
Collapse
Affiliation(s)
| | - Siri Williamson
- Department of Chemistry, Carleton University, Ottawa, Ontario K1S 5B6, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada
| | | |
Collapse
|
2
|
Nickerson CJ, Bryenton KR, Price AJA, Johnson ER. Comparison of Density-Functional Theory Dispersion Corrections for the DES15K Database. J Phys Chem A 2023; 127:8712-8722. [PMID: 37793049 DOI: 10.1021/acs.jpca.3c04332] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023]
Abstract
While density-functional theory (DFT) remains one of the most widely used tools in computational chemistry, most functionals fail to properly account for the effects of London dispersion. Hence, there are many popular post-self-consistent methods to add a dispersion correction to the DFT energy. Until now, the most popular methods have never been compared on equal footing due to not being implemented in the same electronic structure packages. In this work, we performed a large-scale benchmarking study, directly comparing the accuracy of the exchange-hole dipole moment (XDM), D3BJ, D4, TS, MBD, and MBD-NL dispersion models when applied to the recent DES15K database of nearly 15,000 molecular complexes at both expanded and compressed geometries. Our study showed similarly good performance for all dispersion methods (except TS) when applied to neutral complexes. However, they all performed worse for ionic complexes, particularly those involving dications of alkaline earth metals, due to systematic overbinding by the base PBE0 density functional. Investigation of the largest outliers also revealed that only the MBD and MBD-NL methods demonstrate surprising errors for complexes involving alkali metal cations at compressed geometries where they tended to significantly overbind. As we would expect minimal dispersion binding for such complexes, we further investigated the origins of these errors for the potential energy curve of a model cation-π complex. Overall, there is little choice between the XDM, D3BJ, D4, MBD, and MBD-NL dispersion methods for most systems. However, the MBD-based methods are not recommended for complexes involving organic species and alkali or alkaline earth metal cations, for example when modeling Li+ intercalation into graphite.
Collapse
Affiliation(s)
- Cameron J Nickerson
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Kyle R Bryenton
- Department of Physics and Atmospheric Science, Dalhousie University, 6310 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Alastair J A Price
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| | - Erin R Johnson
- Department of Chemistry, Dalhousie University, 6274 Coburg Rd, Halifax, Nova Scotia B3H 4R2, Canada
| |
Collapse
|
3
|
Sussardi AN, Turner GF, Richardson JG, Spackman MA, Turley AT, McGonigal PR, Jones AC, Moggach SA. Tandem High-Pressure Crystallography-Optical Spectroscopy Unpacks Noncovalent Interactions of Piezochromic Fluorescent Molecular Rotors. J Am Chem Soc 2023; 145:19780-19789. [PMID: 37649399 DOI: 10.1021/jacs.3c05444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
To develop luminescent molecular materials with predictable and stimuli-responsive emission, it is necessary to correlate changes in their geometries, packing structures, and noncovalent interactions with the associated changes in their optical properties. Here, we demonstrate that high-pressure single-crystal X-ray diffraction can be combined with high-pressure UV-visible absorption and fluorescence emission spectroscopies to elucidate how subtle changes in structure influence optical outputs. A piezochromic aggregation-induced emitter, sym-heptaphenylcycloheptatriene (Ph7C7H), displays bathochromic shifts in its absorption and emission spectra at high pressure. Parallel X-ray measurements identify the pressure-induced changes in specific phenyl-phenyl interactions responsible for the piezochromism. Pairs of phenyl rings from neighboring molecules approach the geometry of a stable benzene dimer, while conformational changes alter intramolecular phenyl-phenyl interactions correlated with a relaxed excited state. This tandem crystallographic and spectroscopic analysis provides insights into how subtle structural changes relate to the photophysical properties of Ph7C7H and could be applied to a library of similar compounds to provide general structure-property relationships in fluorescent organic molecules with rotor-like geometries.
Collapse
Affiliation(s)
- Alif N Sussardi
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FL, U.K
| | - Gemma F Turner
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | | | - Mark A Spackman
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| | - Andrew T Turley
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
| | - Paul R McGonigal
- Department of Chemistry, Durham University, Durham DH1 3LE, U.K
- School of Chemistry, The University of York, York YO10 5DD, U.K
| | - Anita C Jones
- School of Chemistry, The University of Edinburgh, Edinburgh EH9 3FL, U.K
| | - Stephen A Moggach
- School of Molecular Sciences, The University of Western Australia, Crawley, Perth 6009, Australia
| |
Collapse
|
4
|
Du P, Yuan H, Tan D, Yang R. Identification of biomolecule-based electronic materials from a first-principles study of aliphatic amino acids. Phys Chem Chem Phys 2023; 25:5520-5528. [PMID: 36723358 DOI: 10.1039/d2cp05333k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Biomolecule-based electronic materials can enable health innovations by virtue of their intrinsic bioactivity and physical properties. However, the ultra-wide bandgap and limited piezoelectric properties of most biomaterials prevent them from reaching their full potential. Herein, the electronic structures and electromechanical properties of aliphatic amino acid crystals are investigated based on density functional theory. L-Met is found to be a wide bandgap p-type semiconductor, and the much-reduced bandgap of 2.88 eV is ascribed to the sulphur atoms in L-Met. L-Leu has a shear piezoelectric voltage constant of 2.706 V mN-1 that is over an order of magnitude higher than that of lead zirconate titanate, and good toughness and ductility are also revealed in L-Leu from mechanical property investigations. This study illustrates a computational approach to find smart and multifunctional biomaterials and inspire their growth and applications.
Collapse
Affiliation(s)
- Pei Du
- School of Advanced Materials and Nanotechnology, Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an 710126, China.
| | - Hui Yuan
- School of Advanced Materials and Nanotechnology, Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an 710126, China. .,Department of Molecular Microbiology and Biotechnology, The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Dan Tan
- School of Advanced Materials and Nanotechnology, Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an 710126, China.
| | - Rusen Yang
- School of Advanced Materials and Nanotechnology, Academy of Advanced Interdisciplinary Research, Xidian University, Xi'an 710126, China.
| |
Collapse
|
5
|
Lu J, Jiang G, Zhang H, Qian B, Zhu H, Gu Q, Yan Y, Liu JZ, Freeman BD, Jiang L, Wang H. An artificial sodium-selective subnanochannel. SCIENCE ADVANCES 2023; 9:eabq1369. [PMID: 36706186 PMCID: PMC9882983 DOI: 10.1126/sciadv.abq1369] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 12/23/2022] [Indexed: 06/18/2023]
Abstract
Single-ion selectivity with high precision has long been pursued for fundamental bioinspired engineering and applications such as in ion separation and energy conversion. However, it remains a challenge to develop artificial ion channels to achieve single-ion selectivity comparable to their biological analogs, especially for high Na+/K+ selectivity. Here, we report an artificial sodium channel by subnanoconfinement of 4'-aminobenzo-15-crown-5 ethers (15C5s) into ~6-Å-sized metal-organic framework subnanochannel (MOFSNC). The resulting 15C5-MOFSNC shows an unprecedented Na+/K+ selectivity of tens to 102 and Na+/Li+ selectivity of 103 under multicomponent permeation conditions, comparable to biological sodium channels. A co-ion-responsive single-file transport mechanism in 15C-MOFSNC is proposed for the preferential transport of Na+ over K+ due to the synergetic effects of size exclusion, charge selectivity, local hydrophobicity, and preferential binding with functional groups. This study provides an alternative strategy for developing potential single-ion selective channels and membranes for many applications.
Collapse
Affiliation(s)
- Jun Lu
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Gengping Jiang
- Department of Applied Physics, College of Science, Wuhan University of Science and Technology, Wuhan 430072, China
| | - Huacheng Zhang
- Chemical and Environmental Engineering, School of Engineering, RMIT University, Melbourne, Victoria 3000, Australia
| | - Binbin Qian
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Haijin Zhu
- Institute for Frontier Materials, Deakin University Waurn Ponds Campus, Geelong, Victoria 3216, Australia
| | - Qinfen Gu
- ANSTO, Australian Synchrotron, 800 Blackburn Rd., Clayton, Victoria 3168, Australia
| | - Yuan Yan
- Department of Mechanical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jefferson Zhe Liu
- Department of Mechanical Engineering, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Benny D. Freeman
- Department of Chemical Engineering, The University of Texas at Austin, Austin, TX, USA
| | - Lei Jiang
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Huanting Wang
- Department of Chemical and Biological Engineering, Monash University, Clayton, Victoria 3800, Australia
| |
Collapse
|
6
|
Bashir M, Dar AA, Yousuf I. Syntheses, Structural Characterization, and Cytotoxicity Assessment of Novel Mn(II) and Zn(II) Complexes of Aroyl-Hydrazone Schiff Base Ligand. ACS OMEGA 2023; 8:3026-3042. [PMID: 36713712 PMCID: PMC9878661 DOI: 10.1021/acsomega.2c05927] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Accepted: 12/30/2022] [Indexed: 06/15/2023]
Abstract
This work describes the syntheses, structural characterization, and biological profile of Mn(II)- and Zn(II)-based complexes 1 and 2 derived from the aroyl-hydrazone Schiff base ligand (L1). The synthesized compounds were thoroughly characterized by elemental analysis, Fourier transform infrared spectroscopy (FTIR), UV-vis, electron paramagnetic resonance (EPR), nuclear magnetic resonance (NMR), and single-crystal X-ray diffraction (s-XRD). Density functional theory (DFT) studies of complexes 1 and 2 were performed to ascertain the structural and electronic properties. Hirshfeld surface analysis was used to investigate different intermolecular interactions that define the stability of crystal lattice structures. To ascertain the therapeutic potential of complexes 1 and 2, in vitro interaction studies were carried out with ct-DNA and bovine serum albumin (BSA) using analytical and multispectroscopic techniques, and the results showed more avid binding of complex 2 than complex 1 and L1. The antioxidant potential of complexes 1 and 2 was examined against the 2,2-diphenyl picrylhydrazyl (DPPH) free radical, which revealed better antioxidant ability of the Mn(II) complex. Moreover, the antibacterial activity of synthesized complexes 1 and 2 was tested against Gram-positive and Gram-negative bacteria in which complex 2 demonstrated more effective bactericidal activity than L1 and complex 1 toward Gram-positive bacteria. Furthermore, the in vitro cytotoxicity assessment of L1 and complexes 1 and 2 was carried out against MDA-MB-231 (triple negative breast cancer) and A549 (lung) cancer cell lines. The cytotoxic results revealed that the polymeric Zn(II) complex exhibited better and selective cytotoxicity against the A549 cancer cell line as was evidenced by its low IC50 value.
Collapse
Affiliation(s)
- Masrat Bashir
- Department
of Chemistry, Aligarh Muslim University, Aligarh202002, Uttar Pradesh, India
| | - Aijaz A. Dar
- Department
of Chemistry, University of Kashmir, Hazratbal, Srinagar190006, Jammu & Kashmir, India
| | - Imtiyaz Yousuf
- Department
of Chemistry, Aligarh Muslim University, Aligarh202002, Uttar Pradesh, India
| |
Collapse
|
7
|
Synthesis, structural characterization and in vitro cytotoxicity assessment of new mononuclear Cu(II) and Co(II) complexes against MDA–MB–231, HCC–1806 and HT–29 cancer cell lines. Polyhedron 2023. [DOI: 10.1016/j.poly.2022.116189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
|
8
|
Rogers FJM, Radhanpura K, Horvat J, Farrant D. On the use of a volume constraint to account for thermal expansion effects on the low-frequency vibrations of molecular crystals. Phys Chem Chem Phys 2022; 24:10408-10419. [PMID: 35441620 DOI: 10.1039/d1cp05718a] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
A volume-constraint method is presented as a means to capture the influence of thermal expansion on the low-frequency vibrations in molecular crystals. In particular, the room-temperature terahertz absorption spectra of L-tartaric acid, α-lactose monohydrate, and α-para-aminobenzoic acid (PABA) have been simulated using dispersion-corrected, solid-state density functional theory (DFT-D). By comparing the normal modes obtained with a unit cell optimised without constraints to those obtained with a unit cell optimised while constrained to keep its experimental volume, wholesale improvements to the resultant spectrum is achieved when using the constrained geometry by inhibiting cell contraction. These improvements are demonstrated over a range of popular density functionals and basis sets up to triple-zeta complexity. A correlation method is then presented as a means to quantitatively compare the vibrational pattern of normal modes obtained from both unit cells. This analysis reveals that thermal expansion can effect the character and relative frequency of normal modes, with the choice of geometry ultimately affecting the assignment of the experimental absorptions. The sensibility of using the experimental volume as an approximation is then discussed, where it is speculated that large basis sets or hybrid functionals are necessary to ensure that the thermal expansion effect is not overestimated. The low-frequency absorption spectrum of PABA is then fully characterised using the PBE-D3BJ/6-311G(2d,2p) method.
Collapse
Affiliation(s)
- Fergus J M Rogers
- Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory 0200, Australia
| | - Krunal Radhanpura
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, NSW 2070, Australia
| | - Joseph Horvat
- School of Physics and Institute for Superconducting and Electronic Materials, University of Wollongong, Wollongong, NSW, 2522, Australia
| | - David Farrant
- Commonwealth Scientific and Industrial Research Organisation (CSIRO), Lindfield, NSW 2070, Australia
| |
Collapse
|
9
|
Bashir M, Yousuf I, Prakash Prasad C. Mixed Ni(II) and Co(II) complexes of nalidixic acid drug: Synthesis, characterization, DNA/BSA binding profile and in vitro cytotoxic evaluation against MDA-MB-231 and HepG2 cancer cell lines. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120910. [PMID: 35077983 DOI: 10.1016/j.saa.2022.120910] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 01/06/2022] [Accepted: 01/15/2022] [Indexed: 06/14/2023]
Abstract
In this work, herein we report the synthesis, structural characterization and in vitro cytotoxic evaluation of two mixed Co(II)/Ni(II)-nalidixic acid-bipyridyl complexes (1 and 2). The structural analysis of metal complexes 1 and 2 was carried out by analytical and multispectroscopic techniques (FT-IR, UV-vis, EPR, sXRD). The crystallographic details of complexes 1 and 2 revealed a monoclinic crystal system with P21/c space group. DFT studies of complexes were performed to get electronic structure and localization of HOMO and LUMO electron densities. Hirshfeld surface analysis of metal complexes 1 and 2 was employed to understand the various intermolecular interactions (C-H···O, N-H···H and O-H···O) that define the stability of crystal lattice structures. The comparative interaction studies of complex 1 and complex 2 with DNA/BSA were performed by diverse multispectroscopic and analytical techniques to evaluate their chemotherapeutic potential. The magnitude of the DNA binding propensity and binding mode was verified by calculating Kb, K and Ksv values. Higher binding affinity was observed in case of complex 2via intercalative mode. Furthermore, the cytotoxic assessment of complexes 1 and 2 was examined against MDA-MB-231 (triple negative human breast cancer cell line) and HepG2 (liver carcinoma cell line) employing MTT assay which revealed remarkably effecient and specific cytotoxic activity of complex 2.
Collapse
Affiliation(s)
- Masrat Bashir
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India
| | - Imtiyaz Yousuf
- Department of Chemistry, Aligarh Muslim University, Aligarh 202002, Uttar Pradesh, India.
| | | |
Collapse
|
10
|
Leloire M, Walshe C, Devaux P, Giovine R, Duval S, Bousquet T, Chibani S, Paul JF, Moissette A, Vezin H, Nerisson P, Cantrel L, Volkringer C, Loiseau T. Capture of Gaseous Iodine in Isoreticular Zirconium-Based UiO-n Metal-Organic Frameworks: Influence of Amino Functionalization, DFT Calculations, Raman and EPR Spectroscopic Investigation. Chemistry 2022; 28:e202104437. [PMID: 35142402 DOI: 10.1002/chem.202104437] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Indexed: 01/09/2023]
Abstract
A series of Zr-based UiO-n MOF materials (n=66, 67, 68) have been studied for iodine capture. Gaseous iodine adsorption was collected kinetically from a home-made set-up allowing the continuous measurement of iodine content trapped within UiO-n compounds, with organic functionalities (-H, -CH3 , -Cl, -Br, -(OH)2 , -NO2 , -NH2 , (-NH2 )2 , -CH2 NH2 ) by in-situ UV-Vis spectroscopy. This study emphasizes the role of the amino groups attached to the aromatic rings of the ligands connecting the {Zr6 O4 (OH)4 } brick. In particular, the preferential interaction of iodine with lone-pair groups, such as amino functions, has been experimentally observed and is also based on DFT calculations. Indeed, higher iodine contents were systematically measured for amino-functionalized UiO-66 or UiO-67, compared to the pristine material (up to 1211 mg/g for UiO-67-(NH2 )2 ). However, DFT calculations revealed the highest computed interaction energies for alkylamine groups (-CH2 NH2 ) in UiO-67 (-128.5 kJ/mol for the octahedral cavity), and pointed out the influence of this specific functionality compared with that of an aromatic amine. The encapsulation of iodine within the pore system of UiO-n materials and their amino-derivatives has been analyzed by UV-Vis and Raman spectroscopy. We showed that a systematic conversion of molecular iodine (I2 ) species into anionic I- ones, stabilized as I- ⋅⋅⋅I2 or I3 - complexes within the MOF cavities, occurs when I2 @UiO-n samples are left in ambient light.
Collapse
Affiliation(s)
- Maeva Leloire
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Catherine Walshe
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Philippe Devaux
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Raynald Giovine
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Sylvain Duval
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Till Bousquet
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Siwar Chibani
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Jean-Francois Paul
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Alain Moissette
- Laboratoire de Spectroscopie pour les Interactions la Réactivité et l'Environnement, Université de Lille, UMR CNRS 8516-LASIRE, 59000, Lille, France
| | - Hervé Vezin
- Laboratoire de Spectroscopie pour les Interactions la Réactivité et l'Environnement, Université de Lille, UMR CNRS 8516-LASIRE, 59000, Lille, France
| | - Philippe Nerisson
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN) PSN-RES, 13115, Saint Paul lez Durance, France
| | - Laurent Cantrel
- Institut de Radioprotection et de Sûreté Nucléaire (IRSN) PSN-RES, 13115, Saint Paul lez Durance, France
| | - Christophe Volkringer
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| | - Thierry Loiseau
- Unité de Catalyse et Chimie du Solide, Université de Lille, Centrale Lille Université d'Artois, UMR CNRS 8181-UCCS, 59000, Lille, France
| |
Collapse
|
11
|
Synthesis, structural characterization and in vitro cytotoxic evaluation of mixed Cu(II)/Co(II) levofloxacin–bipyridyl complexes. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120757] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
|
12
|
Stennett CR, Bursch M, Fettinger JC, Grimme S, Power PP. Designing a Solution-Stable Distannene: The Decisive Role of London Dispersion Effects in the Structure and Properties of {Sn(C 6H 2-2,4,6-Cy 3) 2} 2 (Cy = Cyclohexyl). J Am Chem Soc 2021; 143:21478-21483. [PMID: 34905362 DOI: 10.1021/jacs.1c09976] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The reaction of 1 equiv of the dimeric lithium salt of a new London dispersion effect donor ligand {Li(C6H2-2,4,6-Cy3)·OEt2}2 (Cy = cyclohexyl) with SnCl2 afforded the distannene {Sn(C6H2-2,4,6-Cy3)2}2 (1). The distannene remains dimeric in solution, as indicated by its room-temperature 119Sn NMR signal (δ = 361.3 ppm) and its electronic spectrum, which is invariant over the temperature range of -10 to 100 °C. The formation of the distannene, which has a short Sn-Sn distance of 2.7005(7) Å and greatly enhanced stability in solution compared to that of other distannenes, is due to increased interligand London dispersion (LD) attraction arising from multiple close approaches of ligand C-H moieties across the Sn-Sn bond. DFT-D4 calculations revealed a dispersion stabilization of dimer 1 of 38 kcal mol-1 and a dimerization free energy of ΔGdimer = -6 kcal mol-1. In contrast, the reaction of 2 equiv of the similarly shaped but less bulky, less hydrogen-rich Li(C6H2-2,4,6-Ph3)·(OEt2)2 with SnCl2 yielded the monomeric stannylene Sn(C6H2-2,4,6-Ph3)2 (2), which is unstable in solution at ambient temperature.
Collapse
Affiliation(s)
- Cary R Stennett
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - James C Fettinger
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms-Universität Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Philip P Power
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
13
|
Zehra S, Cirilli I, Silvestri S, Gómez-Ruiz S, Tabassum S, Arjmand F. Structure elucidation, in vitro binding studies and ROS-dependent anti-cancer activity of Cu(II) and Zn(II) phthaloylglycinate(phen) complexes against MDA-MB-231 cells. Metallomics 2021; 13:6415206. [PMID: 34724067 DOI: 10.1093/mtomcs/mfab064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 10/21/2021] [Indexed: 12/24/2022]
Abstract
New mononuclear Cu(II) and Zn(II)-based complexes 1 [Cu(L)2(diimine)HOCH3] and 2 [Zn(L)2(diimine)] have been synthesized as anti-cancer chemotherapeutics targeted to tRNA. The structure elucidation of complexes 1 and 2 was carried out by spectroscopic and single X-ray diffraction studies. In vitro interaction studies of complexes 1 and 2 with ct-DNA/tRNA were performed by employing various biophysical techniques to evaluate and predict their interaction behavior and preferential selectivity at biomolecular therapeutic targets. The corroborative results of the interaction studies demonstrated that complexes 1 and 2 exhibited avid binding propensity via intercalative mode of binding toward ct-DNA/tRNA. Electrophoretic assay revealed that the complexes 1 and 2 were able to promote single- and double-strand cleavage of the plasmid DNA at low micromolar concentrations under physiological conditions in the absence of an additional oxidizing or reducing agent. RNA hydrolysis studies revealed that the complexes 1 and 2 could promote tRNA cleavage in a concentration and time-dependent manner. The cytotoxic potential of complexes 1 and 2 was evaluated against the MDA-MB-231 cell line, which showed that the complexes were able to inhibit the cell growth in a dose-dependent manner. The intracellular ROS production and mitochondrial superoxide anion assay revealed that the complexes 1 and 2 induce a dose-dependent activity, suggesting the involvement of ROS-mediated mitochondrial apoptotic pathway leading to cell death.
Collapse
Affiliation(s)
- Siffeen Zehra
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Ilenia Cirilli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy.,School of Pharmacy, University of Camerino, Camerino (MC) 62032, Italy
| | - Sonia Silvestri
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona 60131, Italy
| | - Santiago Gómez-Ruiz
- COMET-NANO Group, Departamento de Biología y Geología, Física y Química Inorgánica,, E.S.C.E.T., Universidad Rey Juan Carlos, 28933 Móstoles, Madrid, Spain
| | - Sartaj Tabassum
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, UP 202002, India
| |
Collapse
|
14
|
Li Y, Meijer EJ, Liao R. Elucidating the Role of Aqueous Solvent in an Iron‐Based Water Oxidation System by DFT‐based Molecular Simulation. ChemCatChem 2021. [DOI: 10.1002/cctc.202100616] [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]
Affiliation(s)
- Ying‐Ying Li
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Luoyu Road 1037 Wuhan 430074 P. R. China
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam (The Netherlands
| | - Evert Jan Meijer
- Van't Hoff Institute for Molecular Sciences University of Amsterdam Science Park 904 1098 XH Amsterdam (The Netherlands
| | - Rong‐Zhen Liao
- Key Laboratory of Material Chemistry for Energy Conversion and Storage Ministry of Education Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica Hubei Key Laboratory of Materials Chemistry and Service Failure School of Chemistry and Chemical Engineering Huazhong University of Science and Technology Luoyu Road 1037 Wuhan 430074 P. R. China
| |
Collapse
|
15
|
Goloveshkin AS, Korlyukov AA, Vologzhanina AV. Novel Polymorph of Favipiravir-An Antiviral Medication. Pharmaceutics 2021; 13:139. [PMID: 33494498 PMCID: PMC7911870 DOI: 10.3390/pharmaceutics13020139] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 01/15/2021] [Accepted: 01/18/2021] [Indexed: 01/18/2023] Open
Abstract
Various solid forms of pharmaceutically important compounds exhibit different physical properties and bioactivity; thus, knowledge of the structural landscape and prediction of spontaneous polymorph transformations for an active pharmaceutical ingredient is of practical value for the pharmaceutical industry. By recrystallization from ethyl acetate, a novel polymorph of 6-fluoro-3-hydroxypyrazine-2-carboxamide (trademark favipiravir, RNA polymerase inhibitor) was obtained and characterized using differential scanning calorimetry (DSC), infra-red spectroscopy and powder X-ray diffraction (XRD) analysis. The favipiravir molecule in two polymorphs realizes similar H-bonding motifs, but the overall H-bonded networks differ. Based on periodic density functional theory calculations, the novel tetragonal polymorph with two interpenetrated H-bonded networks is slightly less stable than the orthorhombic one with the zst topology of the underlying H-bonded net that is in accord with experimentally observed powder XRD patterns of slow conversion of the tetragonal phase to the orthorhombic one. However, topological analysis of net relations revealed that no transformations can be applied to convert H-bonded networks in the experimental unit cells, and DSC data indicate no solid-state reactions at heating.
Collapse
Affiliation(s)
- Alexander S. Goloveshkin
- A. N. Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova str, 119991 Moscow, Russia; (A.S.G.); (A.A.K.)
| | - Alexander A. Korlyukov
- A. N. Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova str, 119991 Moscow, Russia; (A.S.G.); (A.A.K.)
- Higher Chemical College of the Russian Academy of Sciences, D.M. Mendeleev University of Chemical Technology of Russia, Miusskaya sq. 9, 125047 Moscow, Russia
| | - Anna V. Vologzhanina
- A. N. Nesmeyanov Institute of Organoelement Compounds of the Russian Academy of Sciences, 28 Vavilova str, 119991 Moscow, Russia; (A.S.G.); (A.A.K.)
| |
Collapse
|
16
|
Kiely E, Zwane R, Fox R, Reilly AM, Guerin S. Density functional theory predictions of the mechanical properties of crystalline materials. CrystEngComm 2021. [DOI: 10.1039/d1ce00453k] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The DFT-predicted mechanical properties of crystalline materials are crucial knowledge for their screening, design, and exploitation.
Collapse
Affiliation(s)
- Evan Kiely
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland
| | - Reabetswe Zwane
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Robert Fox
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Anthony M. Reilly
- School of Chemical Sciences, Dublin City University (DCU), Glasnevin, D09 C7F8 Dublin, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| | - Sarah Guerin
- Department of Physics, Bernal Institute, University of Limerick, V94 T9PX, Ireland
- SSPC, Science Foundation Ireland Research Centre for Pharmaceuticals, University of Limerick, V94 T9PX, Ireland
| |
Collapse
|
17
|
Zehra S, Gómez-Ruiz S, Siddique HR, Tabassum S, Arjmand F. Water soluble ionic Co(II), Cu(II) and Zn(II) diimine-glycinate complexes targeted to tRNA: structural description, in vitro comparative binding, cleavage and cytotoxic studies towards chemoresistant prostate cancer cells. Dalton Trans 2020; 49:16830-16848. [PMID: 33179662 DOI: 10.1039/d0dt02657c] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Four new water soluble Co(ii), Cu(ii) and Zn(ii) ionic metal complexes (1-4) [Cu(diimine)(H2O)2(glycinate)]+[glycinate]-, [Co(diimine)(H2O)4]+[glycinate]- and [Zn(diimine) (H2O)4]+[glycinate]-, where diimine = 2,2'-bipyridine (1-3) and 1,10-phenanthroline (4) were synthesized and thoroughly characterized by spectroscopic and single X-ray crystallographic studies. Complex 1 possesses a triclinic crystal system with a penta-coordinated geometry whereas complexes 2-4 crystallized in an isostructural monoclinic system having distorted octahedral geometry. Density functional theory (DFT) studies for complexes 1-4 were performed to correlate their geometrical parameters and to calculate the energy of frontier molecular orbitals. The corroborative results of spectroscopic and voltammetric studies with ct-DNA and tRNA revealed that the complexes bind noncovalently via an electrostatic mode of binding with specificity for tRNA as compared to ct-DNA. Gel electrophoresis experiments revealed that all the complexes unwind the plasmid pBR322 DNA at low micromolar concentrations (2-9 μM) following an oxidative mechanism for Cu(ii) and Co(ii) complexes (1, 2 and 4) whereas the Zn(ii) complex (3) mediates DNA cleavage by the hydrolytic pathway. The tRNA cleavage showed concentration and time dependent activity of the complexes to promote RNA hydrolysis. Furthermore, the BSA binding ability of complexes 1-4 was monitored, which revealed that the complexes could quench the intrinsic fluorescence in a static manner. Complexes 1-4 were found to be non-toxic towards normal prostate epithelial cells, PNT2, but were potent against chemoresistant metastatic prostate cancer cells, Du145, with GI50 values ranging from 12.75-37 μM. Complexes 1 and 2 also showed cytotoxic activity against cancer stem cells having GI50 values of 14.70 and 14.90 μM, respectively. Molecular docking studies were performed with DNA and tRNA which further validated the spectroscopic analysis demonstrating the higher binding affinity of the complexes towards tRNA.
Collapse
Affiliation(s)
- Siffeen Zehra
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P., India-202002.
| | | | | | | | | |
Collapse
|
18
|
Böttger S, Gruber M, Münzer JE, Bernard GM, Kneusels NJH, Poggel C, Klein M, Hampel F, Neumüller B, Sundermeyer J, Michaelis VK, Tonner R, Tykwinski RR, Kuzu I. Solvent-Induced Bond-Bending Isomerism in Hexaphenyl Carbodiphosphorane: Decisive Dispersion Interactions in the Solid State. Inorg Chem 2020; 59:12054-12064. [DOI: 10.1021/acs.inorgchem.0c00994] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Silas Böttger
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Marco Gruber
- Interdisciplinary Center of Molecular Materials (ICMM), Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nuremberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Jörn Eike Münzer
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Guy M. Bernard
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nis-Julian H. Kneusels
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Christina Poggel
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Marius Klein
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Frank Hampel
- Interdisciplinary Center of Molecular Materials (ICMM), Department of Chemistry and Pharmacy, Friedrich-Alexander-University of Erlangen-Nuremberg (FAU), Nikolaus-Fiebiger-Straße 10, 91058 Erlangen, Germany
| | - Bernhard Neumüller
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Jörg Sundermeyer
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | | | - Ralf Tonner
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| | - Rik R. Tykwinski
- Department of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Istemi Kuzu
- Department of Chemistry, Philipps-University of Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany
| |
Collapse
|
19
|
Costa-Amaral R, Gohda Y. First-principles study of the adsorption of 3d transition metals on BaO- and TiO2-terminated cubic-phase BaTiO3(001) surfaces. J Chem Phys 2020; 152:204701. [DOI: 10.1063/5.0008130] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Rafael Costa-Amaral
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| | - Yoshihiro Gohda
- Department of Materials Science and Engineering, Tokyo Institute of Technology, Yokohama 226-8502, Japan
| |
Collapse
|
20
|
Otero-de-la-Roza A, LeBlanc LM, Johnson ER. What is “many-body” dispersion and should I worry about it? Phys Chem Chem Phys 2020; 22:8266-8276. [DOI: 10.1039/d0cp01213k] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
“Many-body” dispersion can refer to two distinct phenomena, here termed electronic and atomic many-body effects, both of which cause the dispersion energy to be non-additive.
Collapse
Affiliation(s)
- A. Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA-Consolider Team
- Facultad de Química
- Universidad de Oviedo
- 33006 Oviedo
- Spain
| | | | | |
Collapse
|
21
|
He H, Yao G, Ma Y, Feng N, Zhou S, Huang Q. Experimental and Theoretical Study of the Raman Spectra of Ganoderic Acid T. J STRUCT CHEM+ 2019. [DOI: 10.1134/s0022476619090051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
|
22
|
Oswald S, Suhm MA. Soft experimental constraints for soft interactions: a spectroscopic benchmark data set for weak and strong hydrogen bonds. Phys Chem Chem Phys 2019; 21:18799-18810. [PMID: 31453998 DOI: 10.1039/c9cp03651b] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
An experimental benchmark data base on rotational constants, vibrational properties and energy differences for weakly and more strongly hydrogen-bonded complexes and their constituents from the spectroscopic literature is assembled. It is characterized in detail and finally contracted to a more compact, discriminatory set (ENCH-51, for Experimental Non-Covalent Harmonic with 51 entries). The meeting points between theory and experiment consist of equilibrium rotational constants and harmonic frequencies and energies, which are back-corrected from experimental observables and are very easily accessible by quantum chemical calculations. The relative performance of B3LYP-D3, PBE0-D3 and M06-2X density functional theory predictions with a quadruple-zeta basis set is used to illustrate systematic errors, error compensation and selective performance for structural, vibrational and energetical observables. The current focus is on perspectives and different benchmarking methodologies, rather than on a specific theoretical method or a specific class of compounds. Extension of the data base in chemical, observable and quantum chemical method space is encouraged.
Collapse
Affiliation(s)
- Sönke Oswald
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
| | - Martin A Suhm
- Institut für Physikalische Chemie, Universität Göttingen, Tammannstr. 6, 37077 Göttingen, Germany.
| |
Collapse
|
23
|
DL-3-Aminoisobutyric acid: vibrational, NBO and AIM analysis of N-H⋯O bonded-zwitterionic dimer model. Heliyon 2019; 5:e01933. [PMID: 31286081 PMCID: PMC6587070 DOI: 10.1016/j.heliyon.2019.e01933] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2019] [Revised: 05/03/2019] [Accepted: 06/06/2019] [Indexed: 01/18/2023] Open
Abstract
A zwitterionic dimer model constructed of inter-molecular -N-H⋯O bonding has been proposed for the solid sample of DL-3-Aminoisobutyric acid consistent with IR absorption and Raman spectral features measured in the 3500-400/50 cm-1. This zwitterionic dimer model in water as solvent has been computed at B3LYP/6-311++G(d,p) and B3LYP-D3/6-311++G(d,p) levels including Grimme's dispersion correction associated with the -N-H⋯O interaction and SCRF-SMD method. Of the several possible monomer and dimer conformational structures, the most stable dimer constructed of two zwitterion monomer units has produced vibrational modes due to the -NH3 + cation and -CO2‾ anion involved in the -N-H⋯O bonding in fair agreement with the observed broad but composite IR modal features near the 3500-2000 cm-1. Except for the frequency of asymmetric stretching mode of the -NH3 + cation, its symmetric and bending modes agree with the observed values. As for the -CO2‾ anion, the frequencies of all of its modes are in good agreement with the experiment. Natural bond orbital (NBO), molecular electrostatic potential (MEP), atoms-in-molecules (AIM) and non-covalent interaction (NCI) analyses have been used to understand electronic characterization of the -N-H⋯O bonding.
Collapse
|
24
|
Molecular Structures Polymorphism the Role of F…F Interactions in Crystal Packing of Fluorinated Tosylates. CRYSTALS 2019. [DOI: 10.3390/cryst9050242] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The peculiarities of interatomic interactions formed by fluorine atoms were studied in four tosylate derivatives p-CH3C6H4OSO2CH2CF2CF3 and p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5, 7) using X-ray diffraction and quantum chemical calculations. Compounds p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) were crystallized in several polymorph modifications. Analysis of intermolecular bonding was carried out using QTAIM approach and energy partitioning. All compounds are characterized by crystal packing of similar type and the contribution of intermolecular interactions formed by fluorine atoms to lattice energy is raised along with the increase of their amount. The energy of intra- and intermolecular F…F interactions is varied in range 0.5–13.0 kJ/mol. Total contribution of F…F interactions to lattice energy does not exceed 40%. Crystal structures of studied compounds are stabilized mainly by C-H…O and C-H…F weak hydrogen bonds. The analysis of intermolecular interactions and lattice energies in polymorphs of p-CH3C6H4OSO2CH2(CF2)nCHF2 (n = 1, 5) has shown that most stabilized are characterized by the least contribution of F…F interactions.
Collapse
|
25
|
Stöhr M, Van Voorhis T, Tkatchenko A. Theory and practice of modeling van der Waals interactions in electronic-structure calculations. Chem Soc Rev 2019; 48:4118-4154. [PMID: 31190037 DOI: 10.1039/c9cs00060g] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accurate description of long-range electron correlation, most prominently including van der Waals (vdW) dispersion interactions, represents a particularly challenging task in the modeling of molecules and materials. vdW forces arise from the interaction of quantum-mechanical fluctuations in the electronic charge density. Within (semi-)local density functional approximations or Hartree-Fock theory such interactions are neglected altogether. Non-covalent vdW interactions, however, are ubiquitous in nature and play a key role for the understanding and accurate description of the stability, dynamics, structure, and response properties in a plethora of systems. During the last decade, many promising methods have been developed for modeling vdW interactions in electronic-structure calculations. These methods include vdW-inclusive Density Functional Theory and correlated post-Hartree-Fock approaches. Here, we focus on the methods within the framework of Density Functional Theory, including non-local van der Waals density functionals, interatomic dispersion models within many-body and pairwise formulation, and random phase approximation-based approaches. This review aims to guide the reader through the theoretical foundations of these methods in a tutorial-style manner and, in particular, highlight practical aspects such as the applicability and the advantages and shortcomings of current vdW-inclusive approaches. In addition, we give an overview of complementary experimental approaches, and discuss tools for the qualitative understanding of non-covalent interactions as well as energy decomposition techniques. Besides representing a reference for the current state-of-the-art, this work is thus also designed as a concise and detailed introduction to vdW-inclusive electronic structure calculations for a general and broad audience.
Collapse
Affiliation(s)
- Martin Stöhr
- Physics and Materials Science Research Unit, University of Luxembourg, L-1511 Luxembourg, Luxembourg.
| | | | | |
Collapse
|
26
|
Xu S, Sabino FP, Janotti A, Chase DB, Sparks DL, Rabolt JF. Unique Surface Enhanced Raman Scattering Substrate for the Study of Arsenic Speciation and Detection. J Phys Chem A 2018; 122:9474-9482. [PMID: 30418025 DOI: 10.1021/acs.jpca.8b09104] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, a three-dimensional surface enhanced Raman scattering (SERS) substrate comprised of silver coated gold nanorods (Ag/AuNRs) decorated on electrospun polycaprolactone (PCL) fibers has been applied, for the first time, to quantitative analytical measurements on various arsenic species: p-arsanilic acid ( pAsA), roxarsone (Rox), and arsenate (AsV), with a demonstrated sensitivity below 5 ppb. AsV detection in a solution of common salt ions has been demonstrated, showing the tolerance of the substrate to more complex environments. pAsA adsorption behavior on the substrate surface has been investigated in detail using these unique SERS substrates. Calculations based on density functional theory (DFT) support the spectral observation for pAsA. This substrate also has been shown to serve as a platform for in situ studies of arsenic desorption and reduction. This SERS substrate is potentially an excellent environmental sensor for both fundamental studies and practical applications.
Collapse
|
27
|
Sameera WMC, Maseras F. Expanding the Range of Force Fields Available for ONIOM Calculations: The SICTWO Interface. J Chem Inf Model 2018; 58:1828-1835. [PMID: 30137980 DOI: 10.1021/acs.jcim.8b00332] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
The ONIOM scheme is one of the most popular QM/MM approaches, but its extended application has been so far hindered by the limited availability of force fields in most practical implementations. This paper describes a simple software code to overcome this limitation, and its application to three representative chemical problems. The "Shell Interface for Combining Tinker With ONIOM" (SICTWO) program gives access to all force fields available in the Tinker molecular mechanics program from a Gaussian09 or Gaussian16 calculation. The first application presented is the geometry optimization of dithienobicyclo-[4.4.1]-undeca-3,8-diene-11-one ethylene glycol ketal. A variety of force fields were tested for the MM part, and the molecular structure using the ONIOM(B3LYP:OPLS-AA) method shows good agreement with the experimental results. The second problem is related with enantioselectivity of the vanadium-catalyzed asymmetric oxidation of 1,2-bis( tert-butyl)-disulfide. ONIOM(B3LYP:MM3) results, obtained with SICTWO, are consistent with those of a previous IMOMM(B3LYP:MM3) study. In the third application, we have combined AMOEBA09 polarizable force field with ONIOM to study a water molecule binding on water ice. Calculated ONIOM(ωB97X-D:AMOEBA09) binding energies are consistent with the ωB97X-D results. These studies show SICTWO as an easy-to-use tool that can further expand the use of the multiscale ONIOM method within computational chemistry and computational biology.
Collapse
Affiliation(s)
- W M C Sameera
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Institute of Low Temperature Science , Hokkaido University , Sapporo , Hokkaido 060-0819 , Japan
| | - Feliu Maseras
- Institute of Chemical Research of Catalonia (ICIQ) , The Barcelona Institute of Science and Technology , Avgda. Països Catalans 16 , 43007 , Tarragona , Spain.,Departament de Química , Universitat Autònoma de Barcelona , 08193 Bellaterra , Spain
| |
Collapse
|
28
|
McCrea-Hendrick ML, Bursch M, Gullett KL, Maurer LR, Fettinger JC, Grimme S, Power PP. Counterintuitive Interligand Angles in the Diaryls E{C6H3-2,6-(C6H2-2,4,6-iPr3)2}2 (E = Ge, Sn, or Pb) and Related Species: The Role of London Dispersion Forces. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00225] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Madison L. McCrea-Hendrick
- Department of Chemistry, The University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Kelly L. Gullett
- Department of Chemistry, The University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Leonard R. Maurer
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - James C. Fettinger
- Department of Chemistry, The University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University of Bonn, Beringstraße 4, D-53115 Bonn, Germany
| | - Philip P. Power
- Department of Chemistry, The University of California—Davis, 1 Shields Avenue, Davis, California 95616, United States
| |
Collapse
|
29
|
Walters ET, Mohebifar M, Johnson ER, Rowley CN. Evaluating the London Dispersion Coefficients of Protein Force Fields Using the Exchange-Hole Dipole Moment Model. J Phys Chem B 2018; 122:6690-6701. [DOI: 10.1021/acs.jpcb.8b02814] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Evan T. Walters
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Mohamad Mohebifar
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| | - Erin R. Johnson
- Department of Chemistry, Dalhousie University, Halifax B3H 4R2, Nova Scotia, Canada
| | - Christopher N. Rowley
- Department of Chemistry, Memorial University of Newfoundland, St. John’s A1C 5S7, Newfoundland and Labrador, Canada
| |
Collapse
|
30
|
Costa-Amaral R, Da Silva JLF. The adsorption of alcohols on strained Pt3Ni(111) substrates: a density functional investigation within the D3 van der Waals correction. Phys Chem Chem Phys 2018; 20:24210-24221. [DOI: 10.1039/c8cp02874e] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this theoretical study, we address the effect of strain and alloying on the adsorption of methanol, ethanol and glycerol on Pt3Ni(111) surfaces.
Collapse
|
31
|
Chibani S, Badawi M, Loiseau T, Volkringer C, Cantrel L, Paul JF. A DFT study of RuO4 interactions with porous materials: metal–organic frameworks (MOFs) and zeolites. Phys Chem Chem Phys 2018; 20:16770-16776. [DOI: 10.1039/c8cp01950a] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The potential use of zeolite and MOF materials for the capture of RuO4 has been investigated for the first time. A hydrated form of HKUST-1 could be a promising sorbent due to its ability to form multiple hydrogen bonds.
Collapse
Affiliation(s)
| | - Michael Badawi
- Université de Lorraine
- Laboratoire Physique et Chimie Théoriques UMR CNRS 7019
- 57500 Saint-Avold
- France
| | | | | | - Laurent Cantrel
- Institut de Radioprotection et de Sûreté Nucléaire
- CE Cadarache
- F-13115 Saint Paul lez Durance
- France
| | | |
Collapse
|
32
|
Besse R, Da Silva JLF. The role of the alkali and chalcogen atoms on the stability of the layered chalcogenide [Formula: see text] (A = alkali-metal; M = metal-cations; Q = chalcogen) compounds: a density functional theory investigation within van der Waals corrections. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:035402. [PMID: 27849630 DOI: 10.1088/1361-648x/29/3/035402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
There is a great interest to design two-dimensional (2D) chalcogenide materials, however, our atomistic understanding of the major physical parameters that drive the formation of 2D or three-dimensional (3D) chalcogenides is far from satisfactory, in particular, for complex quaternary systems. To address this problem, we selected a set of quaternary 2D and 3D chalcogenide compounds, namely, [Formula: see text] (A = Li, K, Cs; Q = S, Se, Te), which were investigated by density functional theory calculations within van der Waals (vdW) corrections. Employing experimental crystal structures and well designed crystal modifications, we found that the average atomic radius of the alkali-metal, A, and chalcogen, Q, species play a crucial role in the stability of the 2D structures. For example, the 2D structures are energetically favored for smaller [Formula: see text] and larger [Formula: see text] average atomic radius, while 3D structures are favored at intermediate average atomic radius. Those results are explained in terms of strain minimization and Coulomb repulsion of the anionic species in the structure framework. Furthermore, the equilibrium lattice parameters are in excellent agreement with experimental results. Thus, the present insights can help in the design of stable quartenary 2D chalcogenide compounds.
Collapse
Affiliation(s)
- Rafael Besse
- São Carlos Institute of Physics, University of São Paulo, PO Box 369, 13560-970, São Carlos, São Paulo, Brazil
| | | |
Collapse
|
33
|
Tereshchuk P, Amaral RC, Seminovski Y, Da Silva JLF. Glycerol adsorption on a defected Pt6/Pt(100) substrate: a density functional theory investigation within the D3 van der Waals correction. RSC Adv 2017. [DOI: 10.1039/c7ra00976c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
We report an ab initio investigation to obtain an improved atomistic understanding of the adsorption properties of glycerol on a defected Pt6/Pt(100) substrate.
Collapse
Affiliation(s)
- Polina Tereshchuk
- São Carlos Institute of Chemistry
- University of São Paulo
- São Carlos
- Brazil
| | - Rafael C. Amaral
- São Carlos Institute of Chemistry
- University of São Paulo
- São Carlos
- Brazil
| | - Yohanna Seminovski
- São Carlos Institute of Chemistry
- University of São Paulo
- São Carlos
- Brazil
| | | |
Collapse
|
34
|
Kawanami Y, Katsumata SY, Nishijima M, Fukuhara G, Asano K, Suzuki T, Yang C, Nakamura A, Mori T, Inoue Y. Supramolecular Photochirogenesis with a Higher-Order Complex: Highly Accelerated Exclusively Head-to-Head Photocyclodimerization of 2-Anthracenecarboxylic Acid via 2:2 Complexation with Prolinol. J Am Chem Soc 2016; 138:12187-201. [DOI: 10.1021/jacs.6b05598] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | | | | | - Kaori Asano
- Comprehensive
Analysis Center, Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, Ibaraki 567-0047, Japan
| | - Takeyuki Suzuki
- Comprehensive
Analysis Center, Institute of Scientific and Industrial Research, Osaka University, Mihogaoka, Ibaraki 567-0047, Japan
| | - Cheng Yang
- Key Laboratory of Green Chemistry & Technology (Ministry of Education), College of Chemistry, Sichuan University, Wangjiang Road, Chengdu 610064, China
| | - Asao Nakamura
- Department
of Chemistry, College of Engineering, Shibaura Institute of Technology, Saitama-shi 337-8570, Japan
| | | | | |
Collapse
|
35
|
Stegmüller A, Werner K, Reutzel M, Beyer A, Rosenow P, Höfer U, Stolz W, Volz K, Dürr M, Tonner R. Surface Chemistry of tert-
Butylphosphine (TBP) on Si(001) in the Nucleation Phase of Thin-Film Growth. Chemistry 2016; 22:14920-14928. [DOI: 10.1002/chem.201602418] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/12/2022]
Affiliation(s)
- Andreas Stegmüller
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35032 Marburg Germany
| | - Katharina Werner
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Marcel Reutzel
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Andreas Beyer
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Phil Rosenow
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35032 Marburg Germany
| | - Ulrich Höfer
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Wolfgang Stolz
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Kerstin Volz
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
| | - Michael Dürr
- Fachbereich Physik and Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 6 35032 Marburg Germany
- Institut für Angewandte Physik; Justus-Liebig-Universität Giessen; Heinrich-Buff-Ring 16 35392 Giessen Germany
| | - Ralf Tonner
- Fachbereich Chemie und Wissenschaftliches Zentrum für Materialwissenschaften; Philipps-Universität Marburg; Hans-Meerwein-Straße 4 35032 Marburg Germany
| |
Collapse
|
36
|
Tonner R, Rosenow P, Jakob P. Molecular structure and vibrations of NTCDA monolayers on Ag(111) from density-functional theory and infrared absorption spectroscopy. Phys Chem Chem Phys 2016; 18:6316-28. [PMID: 26853185 DOI: 10.1039/c5cp06619k] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The structure and vibrational properties of the metal-organic interface of 1,4,5,8-naphthalene-tetracarboxylic dianhydride (NTCDA) on Ag(111) were analysed using Fourier-transform infrared absorption spectroscopy in conjunction with density functional theory calculations including dispersion forces (PBE-D3). Mode assignments and polarizations as well as molecular distortions were determined for four adsorption geometries of NTCDA on top and bridge sites aligned either parallel or perpendicular to the Ag rows and compared to accurate calculations of the free molecule. This enables an in-depth understanding of surface effects on the computed and experimental vibrational spectra of the adsorbed NTCDA molecule. The molecule-substrate interaction comprises two major and equally important contributions: non-directional van der Waals forces between molecule and surface, and covalent bonding of the acyl oxygen atoms with underlying Ag atoms, which is quantified by charge-transfer analysis. Furthermore, adsorption energy calculations showed that the molecular axis of flat-lying NTCDA is oriented preferably in parallel to the Ag rows. The molecule is subject to particular distortions from the planar gas phase structure with covalent bonding leading to downward bending of the acyl oxygen atoms and Pauli repulsion to upward bending of the carbon core. In parallel, strong buckling of the silver surface was identified. As found in previous studies, the lowest unoccupied molecular orbital (LUMO) of the molecule slips below the Fermi level and becomes partially populated upon adsorption. Excitation of totally symmetric vibrational modes then leads to substantial interfacial dynamical charge transfer, which is convincingly reproduced in the calculated IR spectra.
Collapse
Affiliation(s)
- Ralf Tonner
- Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany. and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, 35032 Marburg, Germany
| | - Phil Rosenow
- Fachbereich Chemie, Philipps-Universität Marburg, 35032 Marburg, Germany.
| | - Peter Jakob
- Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, 35032 Marburg, Germany and Fachbereich Physik, Philipps-Universität Marburg, 35032 Marburg, Germany.
| |
Collapse
|
37
|
Ninković DB, Vojislavljević-Vasilev DZ, Medaković VB, Hall MB, Brothers EN, Zarić SD. Aliphatic–aromatic stacking interactions in cyclohexane–benzene are stronger than aromatic–aromatic interaction in the benzene dimer. Phys Chem Chem Phys 2016; 18:25791-25795. [DOI: 10.1039/c6cp03734h] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.
Collapse
Affiliation(s)
- D. B. Ninković
- Innovation Center of Department of Chemistry
- 11000 Belgrade
- Serbia
- Department of Chemistry
- Texas A&M University at Qatar
| | | | - V. B. Medaković
- Department of Chemistry
- University of Belgrade
- 11000 Belgrade
- Serbia
| | - M. B. Hall
- Department of Chemistry
- Texas A&M University
- College Station
- USA
| | - E. N. Brothers
- Department of Chemistry
- Texas A&M University at Qatar
- Doha
- Qatar
| | - S. D. Zarić
- Department of Chemistry
- Texas A&M University at Qatar
- Doha
- Qatar
- Department of Chemistry
| |
Collapse
|
38
|
Freire RLH, Kiejna A, Da Silva JLF. Adsorption of water and ethanol on noble and transition-metal substrates: a density functional investigation within van der Waals corrections. Phys Chem Chem Phys 2016; 18:29526-29536. [DOI: 10.1039/c6cp05620b] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
We report an extensive density functional theory investigation of water and ethanol adsorption on several Cu-, Pt-, and Au-based substrates including substrates with low-coordinated sites due to intermixing of Pt–Cu and Pt–Au in the topmost surface.
Collapse
Affiliation(s)
| | - Adam Kiejna
- Institute of Experimental Physics
- University of Wrocław
- PL-50-204 Wrocław
- Poland
| | | |
Collapse
|
39
|
Grimme S, Brandenburg JG, Bannwarth C, Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J Chem Phys 2015; 143:054107. [PMID: 26254642 DOI: 10.1063/1.4927476] [Citation(s) in RCA: 531] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.
Collapse
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| |
Collapse
|
40
|
Rutigliano M, Sanna N, Palma A. Multiple approach to model unpaired spin density effects in H-ZSM5 zeolite with extra-framework O atom: H-abstraction reaction from methane. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.10.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
41
|
Reimers JR, Ford MJ, Goerigk L. Problems, successes and challenges for the application of dispersion-corrected density-functional theory combined with dispersion-based implicit solvent models to large-scale hydrophobic self-assembly and polymorphism. MOLECULAR SIMULATION 2015. [DOI: 10.1080/08927022.2015.1066504] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
42
|
Wang GB, Zhao HQ, Zhang ZL, Wang WL, Chen DM. Theoretical Study on Resonance Raman Spectra of Tetraoxaporphyrin Dication by TDDFT Calculation. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1504067] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
|
43
|
Yao G, Zhang J, Huang Q. Conformational and vibrational analyses of meta-tyrosine: An experimental and theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2015; 151:111-123. [PMID: 26125991 DOI: 10.1016/j.saa.2015.06.073] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/18/2014] [Revised: 06/18/2015] [Accepted: 06/22/2015] [Indexed: 06/04/2023]
Abstract
M-tyrosine is one kind of positional isomer of tyrosine which is widely applied in agrichemical, medicinal chemistry, and food science. However, the structural and vibrational features of m-tyrosine have not been reported or systematically investigated. In this work, potential energy surface (PES) calculations were used for searching and determining the stable zwitterionic conformers of m-tyrosine, and the Raman spectra of m-tyrosine and deuterated m-tyrosine were measured and interpreted based on theoretical computation. For the spectral simulation, several DFT-based quantum chemistry (QC) methods were employed, and the M06-2X functional with SMD solvent model was found to be best in reproducing the Raman spectra and geometrical property. As such, this study has not only presented a detailed study of m-tyrosine's vibrational property which is lack in the literature, but also may shed some light on the optimal choice of QC methods for calculation of conformations and vibrational properties of zwitterionic amino acids.
Collapse
Affiliation(s)
- Guohua Yao
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Jingjing Zhang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China
| | - Qing Huang
- Key Laboratory of Ion Beam Bioengineering, Institute of Technical Biology and Agriculture Engineering, Hefei Institutes of Physical Science, Chinese Academy of Sciences and Anhui Province, PR China; University of Science & Technology of China, Hefei, Anhui 230026, PR China.
| |
Collapse
|
44
|
Raupach M, Tonner R. A periodic energy decomposition analysis method for the investigation of chemical bonding in extended systems. J Chem Phys 2015; 142:194105. [DOI: 10.1063/1.4919943] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marc Raupach
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| | - Ralf Tonner
- Fachbereich Chemie, Philipps-Universität Marburg, Hans-Meerwein-Straße, 35032 Marburg, Germany
| |
Collapse
|
45
|
Bohlén M, Bolton K. Conformational studies of poly(vinylidene fluoride), poly(trifluoroethylene) and poly(vinylidene fluoride-co-trifluoroethylene) using density functional theory. Phys Chem Chem Phys 2015; 16:12929-39. [PMID: 24848509 DOI: 10.1039/c4cp01012d] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Different conformations of systems consisting of poly(vinylidene fluoride) (PVDF), poly(trifluoroethylene) (PTrFE) and poly(vinylidene fluoride-co-trifluoroethylene) (P(VDF-TrFE)) were investigated using density functional theory with dispersion correction. It was found that the trans-gauche-trans-gauche' (TGTG') conformation of a single PVDF chain is the lowest energy conformer. Crystals of PVDF were modelled using between two to five chains with up to 12 repeat units in each chain and, in agreement with experiment, structures comprised partly or completely of chains with the TGTG' conformation are more stable than structures built up from chains with all-trans (TTTT) conformation. This indicates that an all-trans segment or chain will not induce the growth of a larger crystal with the same chain conformations. In contrast, the energetically preferred structure of PTrFE chains is an all-trans (TTTT) conformation, and the results indicate that copolymerization of vinylidene fluoride with trifluoroethylene can facilitate the formation of the all-trans PVDF conformations. This is probably due to increased intramolecular repulsion between the fluorine atoms and an increased intermolecular attraction in the crystal structure.
Collapse
Affiliation(s)
- Martin Bohlén
- University of Borås, School of Engineering, Allégatan 1, 501 90 Borås, Sweden.
| | | |
Collapse
|
46
|
Hongo K, Watson MA, Iitaka T, Aspuru-Guzik A, Maezono R. Diffusion Monte Carlo Study of Para-Diiodobenzene Polymorphism Revisited. J Chem Theory Comput 2015; 11:907-17. [DOI: 10.1021/ct500401p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Kenta Hongo
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Mark A. Watson
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Toshiaki Iitaka
- Computational
Astrophysics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Alán Aspuru-Guzik
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ryo Maezono
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| |
Collapse
|
47
|
Hansen A, Bannwarth C, Grimme S, Petrović P, Werlé C, Djukic JP. The thermochemistry of london dispersion-driven transition metal reactions: getting the 'right answer for the right reason'. ChemistryOpen 2014; 3:177-89. [PMID: 25478313 PMCID: PMC4234214 DOI: 10.1002/open.201402017] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Indexed: 11/10/2022] Open
Abstract
Reliable thermochemical measurements and theoretical predictions for reactions involving large transition metal complexes in which long-range intramolecular London dispersion interactions contribute significantly to their stabilization are still a challenge, particularly for reactions in solution. As an illustrative and chemically important example, two reactions are investigated where a large dipalladium complex is quenched by bulky phosphane ligands (triphenylphosphane and tricyclohexylphosphane). Reaction enthalpies and Gibbs free energies were measured by isotherm titration calorimetry (ITC) and theoretically 'back-corrected' to yield 0 K gas-phase reaction energies (ΔE). It is shown that the Gibbs free solvation energy calculated with continuum models represents the largest source of error in theoretical thermochemistry protocols. The ('back-corrected') experimental reaction energies were used to benchmark (dispersion-corrected) density functional and wave function theory methods. Particularly, we investigated whether the atom-pairwise D3 dispersion correction is also accurate for transition metal chemistry, and how accurately recently developed local coupled-cluster methods describe the important long-range electron correlation contributions. Both, modern dispersion-corrected density functions (e.g., PW6B95-D3(BJ) or B3LYP-NL), as well as the now possible DLPNO-CCSD(T) calculations, are within the 'experimental' gas phase reference value. The remaining uncertainties of 2-3 kcal mol(-1) can be essentially attributed to the solvation models. Hence, the future for accurate theoretical thermochemistry of large transition metal reactions in solution is very promising.
Collapse
Affiliation(s)
- Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute of Physical & Theoretical Chemistry, University of Bonn Beringstr. 4-6, 53115 Bonn (Germany) E-mail:
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institute of Physical & Theoretical Chemistry, University of Bonn Beringstr. 4-6, 53115 Bonn (Germany) E-mail:
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute of Physical & Theoretical Chemistry, University of Bonn Beringstr. 4-6, 53115 Bonn (Germany) E-mail:
| | - Predrag Petrović
- Strasbourg Institute of Chemistry, CNRS, UMR 7177, Laboratory of Chemistry & Organometallic Systems, University of Strasbourg 4 rue Blaise Pascal, 67000 Strasbourg (France) E-mail:
| | - Christophe Werlé
- Strasbourg Institute of Chemistry, CNRS, UMR 7177, Laboratory of Chemistry & Organometallic Systems, University of Strasbourg 4 rue Blaise Pascal, 67000 Strasbourg (France) E-mail:
| | - Jean-Pierre Djukic
- Strasbourg Institute of Chemistry, CNRS, UMR 7177, Laboratory of Chemistry & Organometallic Systems, University of Strasbourg 4 rue Blaise Pascal, 67000 Strasbourg (France) E-mail:
| |
Collapse
|
48
|
Panini P, Venugopala KN, Odhav B, Chopra D. Polymorphism in two biologically active dihydropyrimidinium hydrochloride derivatives: quantitative inputs towards the energetics associated with crystal packing. ACTA CRYSTALLOGRAPHICA SECTION B, STRUCTURAL SCIENCE, CRYSTAL ENGINEERING AND MATERIALS 2014; 70:681-696. [PMID: 25080247 DOI: 10.1107/s2052520614006209] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 03/20/2014] [Indexed: 06/03/2023]
Abstract
A new polymorph belonging to the tetrahydropyrimidinium class of compounds, namely 6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-2-(3-(trifluoromethylthio)phenylamino)-3,6-dihydropyrimidin-1-ium chloride, and a hydrate of 2-(3-bromophenylamino)-6-(4-chlorophenyl)-5-(methoxycarbonyl)-4-methyl-3,6-dihydropyrimidin-1-ium chloride, have been isolated and characterized using single-crystal X-ray diffraction (XRD). A detailed comprehensive analysis of the crystal packing in terms of the associated intermolecular interactions and a quantification of their interaction energies have been performed for both forms of the two different organic salts (A and B) using X-ray crystallography and computational methods such as density functional theory (DFT) quantum mechanical calculations, PIXEL lattice-energy calculations (with decomposition of total lattice energy into the Coulombic, polarization, dispersion and repulsion contribution), the calculation of the Madelung constant (the EUGEN method), Hirshfeld and two-dimensional fingerprint plots. The presence of ionic [N-H](+)···Cl(-) and [C-H](+)···Cl(-) hydrogen bonds mainly stabilizes the crystal packing in both forms A and B, while in the case of B·H2O [N-H](+)···O(water) and O(water)-H···Cl(-) hydrogen bonds along with [N-H](+)···Cl(-) and [C-H](+)···Cl(-) provide stability to the crystal packing. The lattice-energy calculations from both PIXEL and EUGEN methods revealed that in the case of A, form (I) (monoclinic) is more stable whereas for B it is the anhydrous form that is more stable. The analysis of the `Madelung mode' of crystal packing of two forms of A and B and its hydrates suggest that differences exist in the position of the charged ions/atoms in the organic solid state. The R/E (distance-energy) plots for all the crystal structures show that the molecular pairs in their crystal packing are connected with either highly stabilizing (due to the presence of organic R(+) and Cl(-)) or highly destabilizing Coulombic contacts. The difference in crystal packing and associated intermolecular interactions between polymorphs (in the case of A) or the hydrates (in the case of B) have been clearly elucidated by the analysis of Hirshfeld surfaces and two-dimensional fingerprint plots. The relative contributions of the various interactions to the Hirshfeld surface for the cationic (dihydropyrimidinium) part and anionic (chloride ion) part for the two forms of A and B and its hydrate were observed to be different.
Collapse
Affiliation(s)
- Piyush Panini
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| | - K N Venugopala
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Bharti Odhav
- Department of Biotechnology and Food Technology, Durban University of Technology, Durban 4001, South Africa
| | - Deepak Chopra
- Department of Chemistry, Indian Institute of Science Education and Research Bhopal, Madhya Pradesh 462066, India
| |
Collapse
|
49
|
Brémond É, Golubev N, Steinmann SN, Corminboeuf C. How important is self-consistency for the dDsC density dependent dispersion correction? J Chem Phys 2014; 140:18A516. [DOI: 10.1063/1.4867195] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
50
|
Li Y, Pantoja BA, Chen Z. Self-Modulated Band Structure Engineering in C4F Nanosheets: First-Principles Insights. J Chem Theory Comput 2014; 10:1265-71. [DOI: 10.1021/ct401083c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Yafei Li
- College
of Chemistry and Materials Science, Jiangsu Key Laboratory of Biofunctional
Materials, Nanjing Normal University, Nanjing, Jingsu, 210046, China
| | - Bay Allen Pantoja
- Department
of Chemistry, Institute for Functional Nanomaterials, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico 00931
| | - Zhongfang Chen
- Department
of Chemistry, Institute for Functional Nanomaterials, University of Puerto Rico, Rio Piedras Campus, San Juan, Puerto Rico 00931
| |
Collapse
|