1
|
Cheng Y, Verstraelen T. A new framework for frequency-dependent polarizable force fields. J Chem Phys 2022; 157:124106. [PMID: 36182425 DOI: 10.1063/5.0115151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
A frequency-dependent extension of the polarizable force field "Atom-Condensed Kohn-Sham density functional theory approximated to the second-order" (ACKS2) [Verstraelen et al., J. Chem. Phys. 141, 194114 (2014)] is proposed, referred to as ACKS2ω. The method enables theoretical predictions of dynamical response properties of finite systems after partitioning of the frequency-dependent molecular response function. Parameters in this model are computed simply as expectation values of an electronic wavefunction, and the hardness matrix is entirely reused from ACKS2 as an adiabatic approximation is used. A numerical validation shows that accurate models can already be obtained with atomic monopoles and dipoles. Absorption spectra of 42 organic and inorganic molecular monomers are evaluated using ACKS2ω, and our results agree well with the time-dependent DFT calculations. Also for the calculation of C6 dispersion coefficients, ACKS2ω closely reproduces its TDDFT reference. When parameters for ACKS2ω are derived from a PBE/aug-cc-pVDZ ground state, it reproduces experimental values for 903 organic and inorganic intermolecular pairs with an MAPE of 3.84%. Our results confirm that ACKS2ω offers a solid connection between the quantum-mechanical description of frequency-dependent response and computationally efficient force-field models.
Collapse
Affiliation(s)
- YingXing Cheng
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Gent, Belgium
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Gent, Belgium
| |
Collapse
|
2
|
Liang R, Bakhtiiari A. Effects of Enzyme-Ligand Interactions on the Photoisomerization of a Light-Regulated Chemotherapeutic Drug. J Phys Chem B 2022; 126:2382-2393. [PMID: 35297246 DOI: 10.1021/acs.jpcb.1c10819] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular photoswitches permit using light to control protein activity with high spatiotemporal resolutions, thereby alleviating the side effects of conventional chemotherapy. However, due to the challenges in probing ultrafast photoisomerization reactions in biological environments, it remains elusive how the protein influences the photochemistry of the photoswitches, which hampers the rational design of light-regulated therapeutics. To overcome this challenge, we employed first-principles nonadiabatic dynamics simulations to characterize the photodynamics of the phototrexate (PTX), a recently developed photoswitchable anticancer chemotherapeutic that reversibly inhibits its target enzyme dihydrofolate reductase (DHFR). Our simulations show that the protein environment impedes the trans to cis photoisomerization of the PTX. The confinement in the ligand-binding cavity slows down the isomerization kinetics and quantum yield of the photoswitch by reshaping its conical intersection, increasing its excited-state free-energy barrier and quenching its local density fluctuations. Also, the protein environment results in a suboptimal binding mode of the photoproduct that needs to undergo large structural rearrangement to effectively inhibit the enzyme. Therefore, we predict that the PTX's trans → cis photoisomerization in solution precedes its binding with the protein, despite the favorable binding energy of the trans isomer. Our findings highlight the importance of the protein environment on the photochemical reactions of the molecular photoswitches. As such, our work represents an important step toward the rational design of light-regulated drugs in photopharmacology.
Collapse
Affiliation(s)
- Ruibin Liang
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Amirhossein Bakhtiiari
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| |
Collapse
|
3
|
Evaluation of Molecular Polarizability and of Intensity Carrying Modes Contributions in Circular Dichroism Spectroscopies. APPLIED SCIENCES-BASEL 2019. [DOI: 10.3390/app9214691] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
We re-examine the theory of electronic and vibrational circular dichroism spectroscopy in terms of the formalism of frequency-dependent molecular polarizabilities. We show the link between Fermi’s gold rule in circular dichroism and the trace of the complex electric dipole–magnetic dipole polarizability. We introduce the C++ code polar to compute the molecular polarizability complex tensors from quantum chemistry outputs, thus simulating straightforwardly UV-visible absorption (UV-Vis)/electronic circular dichroism (ECD) spectra, and infrared (IR)/vibrational circular dichroism (VCD) spectra. We validate the theory and the code by referring to literature data of a large group of chiral molecules, showing the remarkable accuracy of density functional theory (DFT) methods. We anticipate the application of this methodology to the interpretation of vibrational spectra in various measurement conditions, even in presence of metal surfaces with plasmonic properties. Our theoretical developments aim, in the long run, at embedding the quantum-mechanical details of the chiroptical spectroscopic response of a molecule into the simulation of the electromagnetic field distribution at the surface of plasmonic devices. Such simulations are also instrumental to the interpretation of the experimental spectra measured from devices designed to enhance chiroptical interactions by the surface plasmon resonance of metal nanostructures.
Collapse
|
4
|
Isac DL, Airinei A, Maftei D, Humelnicu I, Mocci F, Laaksonen A, Pinteală M. On the Charge-Transfer Excitations in Azobenzene Maleimide Compounds: A Theoretical Study. J Phys Chem A 2019; 123:5525-5536. [DOI: 10.1021/acs.jpca.9b02082] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dragos Lucian Isac
- “Petru Poni” Institute of Macromolecular Chemistry Iasi, Grigore Ghica Voda Al. No. 41A, 700487 Iasi, Romania
| | - Anton Airinei
- “Petru Poni” Institute of Macromolecular Chemistry Iasi, Grigore Ghica Voda Al. No. 41A, 700487 Iasi, Romania
| | - Dan Maftei
- Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I Blvd. No 11, 700506 Iasi, Romania
| | - Ionel Humelnicu
- Department of Chemistry, “Alexandru Ioan Cuza” University of Iasi, Carol I Blvd. No 11, 700506 Iasi, Romania
| | - Francesca Mocci
- “Petru Poni” Institute of Macromolecular Chemistry Iasi, Grigore Ghica Voda Al. No. 41A, 700487 Iasi, Romania
- Department of Chemical and Geological Sciences, University of Cagliari, I-09042 Monserrato, Italy
| | - Aatto Laaksonen
- “Petru Poni” Institute of Macromolecular Chemistry Iasi, Grigore Ghica Voda Al. No. 41A, 700487 Iasi, Romania
- Department of Materials and Environmental Chemistry, Division of Physical Chemistry, Arrhenius Laboratory, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Mariana Pinteală
- “Petru Poni” Institute of Macromolecular Chemistry Iasi, Grigore Ghica Voda Al. No. 41A, 700487 Iasi, Romania
| |
Collapse
|
5
|
Jones LO, Mosquera MA, Fu B, Schatz GC, Ratner MA, Marks TJ. Germanium Fluoride Nanocages as Optically Transparent n-Type Materials and Their Endohedral Metallofullerene Derivatives. J Am Chem Soc 2019; 141:1672-1684. [PMID: 30608154 DOI: 10.1021/jacs.8b11259] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Carbon- and silicon-based n-type materials tend to suffer from instability of the corresponding radical anions. With DFT calculations, we explore a promising route to overcome such challenges with molecular nanocages which utilize the heavier element Ge. The addition of fluorine substituents creates large electron affinities in the range 2.5-5.5 eV and HOMO-LUMO gaps between 1.6 and 3.2 eV. The LUMOs envelop the surfaces of these structures, suggesting extensive delocalization of injected electrons, analogous to fullerene acceptors. Moreover, these Ge nF n inorganic cages are found to be transparent in the UV-visible region as probed with their excited states. Their capacitance, linear polarizabilities, and dielectric constants are computed and found to be on the same order of magnitude as saturated oligomers and some extended π-organics (azobenzenes). Furthermore, we explore fullerene-type endohedral isomers, i.e., cages with internal substituents or guest atoms, and find them to be more stable than the parent exohedral isomers by up to -206.45 kcal mol-1. We also consider the addition of Li, He, Cs, and Bi, to probe the utility of the exo/ endo cages as host-guest systems. The endohedral He/Li@F8@Ge60F52 cages are significantly more stable than their parent exohedral isomers He/Li@Ge60F52 by -182.46 and -49.22 kcal mol-1, respectively. The energy of formation of endohedral He@F8@Ge60F52 is exothermic by -10.4 kcal mol-1, while Cs and Bi guests are too large to be accommodated but are stable in the exohedral parent cages. Conceivable applications of these materials include n-type semiconductors and transparent electrodes, with potential for novel energy storage modalities.
Collapse
Affiliation(s)
- Leighton O Jones
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Martín A Mosquera
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Bo Fu
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - George C Schatz
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Mark A Ratner
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| | - Tobin J Marks
- Department of Chemistry and the Materials Research Center , Northwestern University , Evanston , Illinois 60208 , United States
| |
Collapse
|
6
|
Davari N, Daub CD, Åstrand PO, Unge M. Local Field Factors and Dielectric Properties of Liquid Benzene. J Phys Chem B 2015; 119:11839-45. [DOI: 10.1021/acs.jpcb.5b07043] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nazanin Davari
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Christopher D. Daub
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Per-Olof Åstrand
- Department
of Chemistry, Norwegian University of Science and Technology (NTNU), NO-7491 Trondheim, Norway
| | - Mikael Unge
- ABB Corporate Research, SE-72178 Västerås, Sweden
| |
Collapse
|
7
|
Davari N, Haghdani S, Åstrand PO, Schatz GC. Local electric field factors by a combined charge-transfer and point–dipole interaction model. RSC Adv 2015. [DOI: 10.1039/c5ra04183j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
A model for the local electric field as a linear response to a frequency-dependent external electric field is presented based on a combined charge-transfer and point–dipole interaction force-field model.
Collapse
Affiliation(s)
- Nazanin Davari
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- Trondheim
- Norway
| | - Shokouh Haghdani
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- Trondheim
- Norway
| | - Per-Olof Åstrand
- Department of Chemistry
- Norwegian University of Science and Technology (NTNU)
- Trondheim
- Norway
| | | |
Collapse
|