Department of Chemistry

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https://hdl.handle.net/10315/2685

Collection consists of research, scholarship and publications produced by graduate students and faculty members of the Department of Chemistry.

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Now showing 1 - 20 of 23

Open Access
Ab-initio investigation of Br-3d core-excited electronic structures of HBr and HBr+
(AIP Publishing, 2019-01-30) Kobayashi, Yuki; Zeng, Tao; Neumark, Daniel M.; Leone, Stephen
Ultrafast X-ray absorption spectroscopy is a powerful tool for real-time probing of chemical dynamics. Interpretation of the time-resolved absorption spectra requires knowledge of core-excited potentials, which necessitates assistance from high-level electronic-structure computations. In this study, we investigate Br-3d core-excited electronic structures of hydrogen bromide (HBr) using the spin-orbit general multiconfigurational quasidegenerate perturbation theory (SO-GMC-QDPT). Core-to-valence excitation energies and transition dipole moments are computed as functions of the internuclear distance for five electronic states of HBr (1Σ0+ , 3Π1, 1Π1, 3Π0+ , 3Π1) and two electronic states of HBr+ (2Π3/2, 2Σ1/2). The results illustrate the capabilities of the Br-3d edge probing to capture transitions of electronic-state symmetry as well as nonadiabatic dissociation processes evolving across avoided crossings. Furthermore, core-to-valence absorption spectra are simulated from the neutral and ionic ground states by numerically solving the time-dependent Schrodinger equation, which exhibit an excellent agreement with an experimental spectrum. The calculated comprehensive and quantitative picture of the core-excited potentials allows for transparent analyses of the core-to-valence absorption signals, filling the gap in the theoretical understanding of the Br-3d absorption spectra.
Open Access
Captodative substitution: a strategy for enhancing the conductivity of molecular electronic devices
(American Chemical Society, 2018) Zeng, Tao; Stuyver, Thijs; Yuta, Tsuji; Fias, Stijn; Geerlings, Paul; De Proft, Frank
We explore a new strategy to tune the conductivity of molecular electronic devices: captodative substitution. We demonstrate that a careful design of such substitution schemes on a benzene parental structure can enhance the conductivity by almost an order of magnitude under small bias. Once this new strategy has been established, we apply it to molecular wires and demonstrate that it enables the unprecedented anti-Ohmic design of wires whose conductivity increases with the length. Overall, the captodative substitution approach provides a very promising pathway toward full chemical control of the conductivity of molecules which opens up the possibility to design molecular switches with an improved on/off ratio among others.
Open Access
A computational study of the protoisomerization of indigo and its imine derivatives
(American Chemical Society, 2016) Zeng, Tao; Hajjar, Laurence; Hicks, Robin;
Abstract: The protoisomerization (isomerization induced by protonation) mechanisms of indigo as well as indigo di- and monoimine derivatives have been investigated using computational chemistry. Both density functional theory (M06-2X) and wave function theory (GMC-QDPT) methods were used to obtain reliable results. A solvation model (CPCM with CH2Cl2 solvent) was employed to mimic the actual environment of the isomerization. The calculations reveal that the protoisomerizations of both the indigo and its imine derivatives are thermodynamically favorable. However, the energy barriers for rotating the double bonds in the derivatives are found to be lower than the one for indigo. More importantly, the imine derivatives undergo one-step isomerization, whereas a twostep process is predicted indigo itself. The computational results provide insightful explanation for the different protoisomerization propensities of the parent indigo and its imine derivatives observed in experiment.
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Controlling thermal stability and volatility of organogold(I) compounds for vapour deposition with complementary ligand design
(Wiley, 2019-11-15) Griffiths, Matthew; Dubrawski, Zack; Bačić, Goran; Japahuge, Achini; Masuda, Jason; Zeng, Tao; Barry, Seán
Atomic layer deposition (ALD) of gold is being studied by multiple research groups, but to date no process using non-energetic oxidizing co-reactants has been demonstrated. In order to access milder co-reactants, precursors with higher thermal stability are required. We set out to uncover how structure and bonding affect the stability and volatility of a family of twelve organogold(I) complexes with a combined X-ray diffraction (XRD), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and density functional theory (DFT) calculations. Small, unsubstituted phosphonium ylide ligands bind more strongly to Au(I) than their silyl-substituted analogues, but their utility suffers due to their high thermal reactivity. Pentafluorophenyl (PFP–) is introduced as a new, very electronegative ligand for gold vapour deposition precursors, and it was found that the penalty to volatility due to pi-stacking and other intermolecular interactions in the solid state is overshadowed by dramatic improvements to the kinetic and thermodynamic stability of complexes of this ligand. Aurophilic interactions are observed for only one compound in this group. We introduce a new figure of merit to compare and rank the suitability of these complexes as precursors for vapour deposition. Finally, DFT calculations on four compounds that have high figures of merit show a linear correlation between the gold-coordinative ligand bond dissociation energies and the observed decomposition points, substantiating this design strategy.
Open Access
Design of singlet fission chromophores with cyclic (alkyl)(amino) carbene building blocks
(AIP Publishing, 2019-06-21) Japahuge, Achini; Lee, Seunghoon; Choi, Cheol Ho; Zeng, Tao
We use MRSF-TDDFT and NEVPT2 methods to design singlet fission chromophores with the building blocks of cyclic (alkyl)(amino)carbenes (CAACs). CAAC dimers with C2, C4, and p-phenylene spacers are considered. The substitutions with trifluoromethyls and fluorine atoms at the α C position are investigated. The electronegative substituents enhance the π accepting capability of the α C, while maintaining it as a quaternary C atom. The phenylene-connected dimers with the two substitutions are identified as promising candidates for singlet fission chromophores. The cylindrically symmetric C2 and C4 spacers allow for substantial structural reorganizations in the S0-to-S1 and S0-to-T1 excitations. Although the two substituted dimers with the C4 spacer satisfy (or very close to satisfy) the primary thermodynamics criterion for singlet fission, the significant structural reorganizations result in high barriers so that the fission is kinetically unfavorable.
Open Access
Design of Small Intramolecular Singlet Fission Chromophore: An Azaborine Candidate and General Small Size Effects
(American Chemical Society, 2016) Zeng, Tao; Goel, Prateek
We report the first attempt to design small intramolecular singlet fission chromophores, with the aid of quantum chemistry and explicitly simulating the time evolution of state populations using quantum dynamics method. We start with three previously proposed azaborine-substituted intermolecular singlet fission chromophores. Through analyzing their frontier orbital amplitudes, we select a BN-substituted azulene as the building block. Covalently connecting two such monomers and tuning their relative configuration, we examine three dimers. One dimer is found to be an eminent candidate: the triplet-pair state is quickly formed within 1 ps, and the two triplets are ready to be disentangled. We elucidate the general small size effects in intramolecular singlet fission and focus on specific aspects which should be taken care of when manipulating the fission rate through steric hindrance.
Open Access
A diabatization protocol that includes spin-orbit coupling
(AIP Publishing, 2017) Zeng, Tao
A diabatization protocol that combines the recently developed model space diabatization scheme and a mean- eld treatment for spin-orbit coupling is presented. The protocol is highly e cient and easy to use. Its robustness is demonstrated in the calculations of the diabatic spin-orbit matrix elements of PH+ 3 , AsH+3 , and SbH+3 . It captures subtle geometry-dependence of the spin-orbit couplings and provides wave function information to explain the origin of the dependence.
Open Access
Diradical Character as a Guiding Principle for the Insightful Design of Molecular Nanowires with an Increasing Conductance with Length
(American Chemical Society, 2018-10-22) Stuyver, Thijs; Zeng, Tao; Tsuji, Yuta; Geerlings, Paul; De Proft, Frank
In recent years, a considerable interest has grown in the design of molecular nanowires with an increasing conductance with length. The development of such nanowires is highly desirable since they could play an important role in future molecular-scale circuitry. Whereas the first experimental observation of this non-classical behaviour still has to be realized, a growing number of candidate wires have been proposed theoretically. In this Letter, we point out that all the wires with an anti-Ohmic increasing conductance with length proposed so far share a common characteristic: their diradical character increases with length. The conceptual connection between diradical character and conductance enables a systematic design of such anti-Ohmic wires and explains the difficulty in their syntheses. A strategy is proposed to balance the stability and conductance, so that this non-classical phenomenon can be observed.
Open Access
Direct imaging of curve-crossing dynamics in IBr by attosecond transient absorption spectroscopy
(American Association for the Advancement of Science, 2019-07-05) Kobayashi, Yuki; Chang, Kristina F.; Zeng, Tao; Neumark, Daniel M.; Leone, Stephen R.
The electronic character of photoexcited molecules can abruptly change at avoided crossings and conical intersections. Here, we report direct spectroscopic imaging of such nonadiabatic processes in a prototype molecule, iodine monobromide (IBr), using extreme-ultraviolet (XUV) attosecond transient absorption spectroscopy. A few-femtosecond visible pulse resonantly excites the B(3Π0+ ) state and the accompanying dissociation dynamics are tracked by an attosecond XUV pulse that simultaneously probes the I-4d and Br-3d core-level ab- sorption edges. Direct comparison with quantum mechanical simulations unambiguously identifies the core-level absorption features associated with adiabatic and diabatic channels at the avoided crossing that is accessed by one-photon and two-photon visible-excitation processes. The results delineate rapid switching of valence-orbital vacancies from σ∗ to π/π∗ ensuing at the avoided crossing.
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Do Diradicals Behave Like Radicals?
(American Chemical Society, 2019-10-08) Stuyver, Thijs; Chen, Bo; Zeng, Tao; Geerlings, Paul; De Proft, Frank; Hoffmann, Roald
This review sets out to understand the reactivity of diradicals, and how that may differ from monoradicals. We also offer a thorough survey and critical evaluation of various measures of diradical character in the literature. The review divides into three parts: 1. We delineate the electronic structure of a diradical with its two degenerate or nearly degenerate singly occupied molecular orbital (SOMO) levels. The well-known appropriate wave functions and energy ordering of low-lying electronic states—one triplet state and three singlet states—of a diradical are introduced. The continuum of electronic structure from diradicals to diradicaloids and finally to closed-shell molecules is described, depending on increasing gaps between the HOMO and LUMO of a molecule. A classification of diradicals based on whether or not the two SOMOs can be located on different sites of the molecule emerges as useful in determining the ground state spin of a diradical. We then move on to a discussion of a delocalized to localized orbital transformation that can be made for the lowest singlet state of diradicals, a transformation that interchanges “closed-shell” to “open-shell” descriptions. The resulting seeming ambiguity in state description is better viewed as a duality, a view that proves to be extremely useful in understanding the dual reactivity of singlet diradicals. 2. In the second, longest part of this paper, we move to reactivity, examining with a consistent level of theory activation energies of prototypical radical reactions -- dimerization, hydrogen abstraction, addition to ethylene -- for some typical organic diradicals and diradicaloids, in their two lowest spin states. The following molecules are studied, and the findings compared to experiment: (1) alkyl chain diradicals vs. alkyl chain radicals: (2) cyclobutadiene vs. 3-cyclobutenyl; (3) trimethylenemethane vs 2-methylallyl; (4) para and meta-quinodimethane vs. benzyl; (5) dioxygen vs peroxyl and hydroxyl. Differences and similarities in reactivity of diradicals vs. monoradicals, based on either a localized or delocalized view, whichever is suitable, are then discussed. The localized perspective seems to work best for radical-type reactions, while the delocalized view is convenient for "closed-shell-type" reactions, such as electrophilic/nucleophilic reactions and concerted pericyclic reactions. The evolution of the exchange integral Kxy along a reaction coordinate plays a determinative role in setting activation energies. The spin densities measure the likelihoods of different sites to undergo radical-like reaction, and the singlet-triplet gap is found to determine the difference between the reaction modes of triplet diradicals and singlet diradical(oid)s. In general, singlet diradical(oid)s exhibit both diradical-like and closed-shell reactivities. 3. The third part of this work begins with an extensive, comparative, and critical survey of available measures of diradical character in the literature. The relationship between diradical character and electron correlation is discussed. We analyze in detail the consequences of diradical character for H2 dissociation, ozone and its sulfur analogues, polyenes, and polyacenes. Finally, we mention briefly, providing leading references, some other types of diradical(oid)s not discussed in detail in the review, such as arynes, main group and transition metal-based diradicals.
Open Access
Electronegativity Seen as the Ground State Average Valence Electron Binding Energy
(American Chemical Society, 2018-11-30) Rahm, Martin; Zeng, Tao; Hoffmann, Roald
We introduce a new electronegativity scale for the atoms, based consistently on ground state energies of valence electrons. The scale is closely related to (yet different from) L.C. Allen’s, which is based on configuration energies. Using a combination of literature experimental values for ground state energies and high level calculated energies where experimental data are missing, we are able to provide electronegativities for elements 1-96. The values are slightly smaller than Allen’s original scale, but correlate well with Allen’s and others. Outliers in agreement with other scales are oxygen and fluorine, now somewhat less electronegative, but in better agreement with their chemistry with the noble gas elements. Groups 11 and 12 electronegativities emerge as high, though Au less so than in other scales. Our scale also gives relatively high electronegativities for Mn, Co, Ni, Zn, Cd, Hg (affected by choice of valence state), and Gd. The new electronegativities provide hints for new alloy/compound design. And a framework is in place to analyze those energy changes in reactions in which electronegativity changes may not be controlling.
Open Access
General formalism for vibronic Hamiltonians in tetragonal symmetry and beyond
(Royal Society of Chemistry, 2018) Zeng, Tao; Hickman, Riley J.; Lang, Robert
We derive general expansion formulas in vibrational coordinates for all bimodal Jahn–Teller and pseudo-Jahn–Teller Hamiltonians in tetragonal symmetry. Symmetry information of all the vibronic Hamiltonian matrix elements is fully carried by up to only 4 eigenvalues of symmetry operators. This problem-to-eigenvalue reduction enables us to handle thousands of vibronic problems in one work. The derived bimodal formulas can be easily extended to cover problems with one or more than two vibrational modes. They lay a solid foundation for future vibronic coupling studies of tetragonal systems. More importantly, the efficient derivation can be applied to handle (pseudo-)Jahn–Teller Hamiltonians for all problems with one principal symmetry axis.
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General formalism of vibronic Hamiltonians for tetrahedral and octahedral systems: problems that involve A-type states and a-type vibrations
(Elsevier, 2018-11-14) Lang, Robert; Japahuge, Achini; Zeng, Tao
In this work, we derive expansion formulas up to arbitrary order in vibrational coordinates for the tetrahedral and octahedral vibronic Hamiltonians that involve A-type states and a-type vibrations. The root-branch approach and modularized approach enable us to derive vibronic Hamiltonians including up to two vibrational modes for 5 problems in T symmetry and 92 problems in Td symmetry within one paper. These formulas can be easily adapted to problems of Th, O, and Oh symmetries. Finishing this work, we have derived general vibronic Hamiltonians for all unimodal and bimodal Jahn-Teller and pseudo-Jahn-Teller problems of cubic group systems. These bimodal formulas can be extended to cover problems that involve more than two modes.
Open Access
General formalism of vibronic Hamiltonians for tetrahedral and octahedral systems: problems that involve T, E states and t, e vibrations
(American Chemical Society, 2017) Zeng, Tao; Hickman, Riley J.; Kadri, Aya; Seidu, Issaka
We derive expansion formulas up to arbitrary order in vibrational coordinates for the tetrahedral and octahedral vibronic Hamiltonians that involve T and E states, and t and e vibrations. These states feature both Jahn–Teller (JT) and pseudo-Jahn–Teller (pJT) effects, and the vibrations are the most JT and pJT active. We first derive the formulas for 92 problems of T and Td symmetries involving up to two vibrational modes. The formulas can be easily generalized to problems of Th, O, and Oh symmetries, as well as problems involving more than two vibrational modes. They can also be adapted to describe spin–orbit vibronic Hamiltonians of tetrahedral p-type problems. Overall, this work makes crucial preparations for future studies on vibronic coupling problems of tetrahedral and octahedral systems. Most importantly, a new, simple, modularized approach to construct vibronic Hamiltonians for a set of related problems, instead of particular problems one by one, is presented.
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Hamiltonian formalism of spin–orbit Jahn–Teller and pseudo-Jahn–Teller problems in trigonal and tetragonal symmetries
(Royal Society of Chemistry, 2019-07-30) Wang, Kun; Zeng, Tao
A formalism for expansions of all bimodal spin-orbit Jahn-Teller and pseudo-Jahn-Teller Hamiltonian operators in trigonal and tetragonal symmetries is presented. With the formalism, we can easily obtain expansion formulas of the Hamiltonian matrix elements in symmetry-adapted vibrational coordinates up to arbitrary order. The formalism is presented as a set of generic matrices and lookup tables, which are convenient to use even without understanding the derivation of the formalism. Three examples are used to demonstrate the correctness, completeness, and conciseness of the formalism. One of the examples is also used to demonstrate how to obtain expansion formulas in more than two vibrational modes by using the bimodal formalism. This work lays a foundation for deriving a unified formalism for spin-orbit and non-spin-orbit (pseudo-)Jahn-Teller Hamiltonians in general axial symmetries.
Open Access
An iodabenzene story
(American Chemical Society, 2017) Zeng, Tao; Rawashdeh, Abdel Monem; Chakkingal Parambil, Priyakumari; Hoffmann, Roald
We call iodabenzene a cyclic (CH)5I molecule. A planar iodabenzene would have 8 π electrons, a situation best avoided by an out-of-plane distortion to a bird-like geometry. The electronic structure and charge distribution of this molecule resemble those of Meisenheimer complexes, derivatives of (CH)5CH2–. A similar substitution strategy, of π-acceptors in ortho and para positions, works in both cases to planarize and stabilize such derivatives. Some 40 kcal/mol (73 kcal/mol for the unsubstituted case) below the bird, a classical 5-iodocyclopentadiene structure awaits, reached through a bicyclic transition state. The calculated activation barrier for the highly exothermic reaction to a classical Lewis structure nevertheless make us optimistic about the chances of detecting and even isolating the bird isomer.
Open Access
Revisiting the (E + A) ⊗ (e + a) problems of polyatomic systems with trigonal symmetry: general expansions of their vibronic Hamiltonians
(Royal Society of Chemistry, 2017) Zeng, Tao; Seidu, Issaka
In this work, we derive general expansions in vibrational coordinates for the (E + A) ⊗ (e + a) vibronic Hamiltonians of molecules with one and only one C3 axis. We first derive the expansion for the lowest C3 symmetry. Additional symmetry elements systematically eliminate terms in the expansion. We compare our expansions with the previous results for two cases, the Image ID:c7cp01171g-t73.gif and the C3 (E + A) ⊗ e. The first comparison demonstrates the robustness, completeness, conciseness, and convenience of our formalism. There is a systematic discrepancy in the second comparison. We discuss the origin of the discrepancy and use a numerical example to corroborate our expansion. Our formalism covers 153 vibronic problems in 6 point groups. It also gives general expansions for the spin–orbit vibronic Hamiltonians of the p-type (E + A) ⊗ (e + a) problems.
Open Access
Structure-function of hydroxyl radical scavenging and chromium-VI reducing cysteinetripeptides derived from rye secalin
(Elsevier, 2018) Zeng, Tao; Leung, Rachel; Venus, Colin; Tsopmo, Apollinaire
This study evaluated for the first time hydroxyl radical scavenging and chromium VI (Cr(VI) reducing properties of four cysteine containing peptides derived from rye secalin. Density functional theory (DFT) calculations were performed to determine the antioxidation mechanism and the effect of residue order. The peptides tested (CQV, QCA, QVC, QCV) were obtained from in silico digestion of rye secalin with Proteinase-K and selected because they contained thiol, a known redox functional group. It was found that at pH 7.4, CQV had the highest Cr(VI) reducing activity (76 %) followed by QCA and QCV (30.8 and 25.5 %, respectively). QVC and GSH had similar but lower activities (11.3 and 11.7%). At pH 3.0, CQV and QCV were found to be less active than the other two peptides. In the hydroxyl radical scavenging assay, CQV had the highest activity with 28.9 ± 1.3 % inhibition of the formation of HO• radicals compared to 19.0 – 13.6% for other peptides. The highest reactivity of CQV with Cr(VI) under neutral conditions was due to the proximity of thiol and amine of glutamine that allowed the formation of a transition state that facilitated the reduction. Cysteine at the N-terminal was important for both the reduction of chromium (pH 7.4) and the HO• scavenging activity because the S-H bond at that position was found by the DFT analysis to have the lowest bond dissociation energy.
Open Access
Theoretical Studies of Singlet Fission: Searching for Materials and Exploring Mechanisms
(Wiley, 2018) Zeng, Tao; Japahuge, Achini
In this Review article, a survey is given for theoretical studies in the subject of singlet fission. Singlet fission converts one singlet exciton to two triplet excitons. With the doubled number of excitons and the longer lifetime of the triplets, singlet fission provides an avenue to improve the photoelectric conversion efficiency in organic photovoltaic devices. It has been a subject of intense research in the past decade. Theoretical studies play an essential role in understanding singlet fission. This article presents a Review of theoretical studies in singlet fission since 2006, the year when the research interest in this subject was reignited. Both electronic structure and dynamics studies are covered. Electronic structure studies provide guidelines for designing singlet fission chromophores and insights into the couplings between single‐ and multi‐excitonic states. The latter provides fundamental knowledge for engineering interchromophore conformations to enhance the fission efficiency. Dynamics studies reveal the importance of vibronic couplings in singlet fission.
Open Access
Through-Linker Intramolecular Singlet Fission: General Mechanism and Designing Small Chromophores
(American Chemical Society, 2016) Zeng, Tao
We perform quantum chemistry calculations and quantum dynamics simulations to investigate the covalent linker’s through-bond effects in intramolecular singlet fission. A model molecule with two diazadiborine chromophore units and the para-phenylene linker is proposed. A general, step-by-step picture for the conversion from the single- to the multiexcitonic state through the linker is presented. On the basis of the picture, we discuss the triplet-pair delocalization into the linker and design two more chromophores with higher fission efficiency. All three designed chromophores have promising picosecond fission time scales and make good candidates for azaborine synthesis.

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