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1.  An exclusive fluoride receptor: Fluoride-induced proton transfer to a quinoline-based thiourea 
Tetrahedron letters  2014;55(8):1467-1470.
A new quinoline-based tripodal thiourea has been synthesized, which exclusively binds fluoride anion in DMSO, showing no affinity for other anions including, chloride, bromide, iodide, perchlorate, nitrate and hydrogen sulfate. As investigated by 1H NMR, the receptor forms both 1:1 and 1:2 complex yielding the binding constants of 2.32(3) (in log β1) and 4.39(4) (in log β2), respectively; where quinoline groups are protonated by the fluoride-induced proton transfer from the solution to the host molecule. The 1:2 binding is due to the interactions of one fluoride with NH binding sites of urea sites and another fluoride with secondary +NH binding sites within the tripodal pocket. The formation of both 1:1 and 1:2 complexes has been confirmed by the theoretical calculations based on density functional theory (DFT).
PMCID: PMC3991426  PMID: 24753636
Fluoride sensor; Thiourea; Anion complex; Molecular recognition; Acyclic receptor
2.  Anomalous Optoelectronic Properties of Chiral Carbon Nanorings…and One Ring to Rule Them All23 
Carbon nanorings are hoop-shaped, π-conjugated macrocycles that form the fundamental annular segments of single-walled carbon nanotubes (SWNTs). In a very recent report, the structures of chiral carbon nanorings (which may serve as chemical templates for synthesizing chiral nanotubes) were experimentally synthesized and characterized for the first time. Here in our Letter we show that the excited-state properties of these unique chiral nanorings exhibit anomalous and extremely interesting optoelectronic properties with excitation energies growing larger as a function of size (in contradiction with typical quantum confinement effects). Although the first electronic excitation in armchair nanorings is forbidden with a weak oscillator strength, we find that the same excitation in chiral nanorings is allowed because of a strong geometric symmetry breaking. Most importantly, among all the possible nanorings synthesized in this fashion, we show that only one ring, corresponding to a SWNT with chiral indices (n+3,n+1), is extremely special with large photoinduced transitions that are most readily observable in spectroscopic experiments.
PMCID: PMC4047598  PMID: 24920994
3.  A Self-assembled Fluoride-Water Cyclic Cluster of [F(H2O)]44− in a Molecular Box 
Journal of the American Chemical Society  2012;134(29):11892-11895.
We present an unprecedented fluoride-water cyclic cluster of [F(H2O)]44− assembled in a cuboid-shaped molecular box formed by two large macrocycles. Structural characterization reveals that the [F(H2O)]44− is assembled by strong H-bonding interactions [OH···F = 2.684(3) to 2.724(3) Å], where a fluoride anion plays the topological role of a water molecule in the classical cyclic water octamer. The interaction of fluoride was further confirmed by 19F NMR and 1H NMR spectroscopies, indicating the encapsulation of the anionic species within the cavity in solution. High level DFT calculations and Bader topological analyses fully support the crystallographic results, demonstrating that the bonding arrangement in the fluoride-water cluster arises from the unique geometry of the host.
PMCID: PMC3601558  PMID: 22765503
4.  Spectroscopic, Structural, and Theoretical Studies of Halide Complexes with a Urea-based Tripodal Receptor 
Inorganic Chemistry  2012;51(7):4274-4284.
A urea-based tripodal receptor L substituted with p-cyanophenyl groups has been studied for halide anions by 1H NMR spectroscopy, density functional theory (DFT) calculations and X-ray crystallography. The 1H NMR titration studies suggest that the receptor forms a 1:1 complex with an anion, showing the binding trend in the order of fluoride > chloride > bromide > iodide. The interaction of fluoride anion with the receptor was further confirmed by 2D NOESY and 19F NMR spectroscopy in DMSO-d6. DFT calculations indicate that the internal halide anion is held by six NH…X interactions with L, showing the highest binding energy for the fluoride complex. Structural characterization of the chloride, bromide, and silicon hexafluoride complexes of [LH+] reveals that the anion is externally located via hydrogen bonding interactions. For the bromide or chloride complex, two anions are bridged with two receptors to form a centrosymmetric dimer, while for the silicon hexafluoride complex, the anion is located within a cage formed by six ligands and two water molecules.
PMCID: PMC3399518  PMID: 22409384
Urea receptor; anion complex; halide binding; hydrogen bonding; fluoride selectivity
5.  A Quinoline Based bis-Urea Receptor for Anions: A Selective Receptor for Hydrogen Sulfate 
Natural Product Communications  2012;7(3):301-304.
A dipodal bis-urea receptor has been synthesized from the reaction of 8-amino quinoline and 1,4-phenylene diisocyanate in dichloromethane, and the anion binding ability of the receptor has been studied using fluoride, chloride, bromide, iodide, perchlorate, nitrate, dihydrogen phosphate and hydrogen sulfate by UV-Vis titrations in DMSO. The results show that the receptor binds each of the anions with a 1:1 stoichiometry, showing high affinity, and moderate selectivity for hydrogen sulfate among the anions studied. Ab initio calculations based on density functional theory (DFT) suggest that an anion (X−) is bonded within the cleft formed by the two arms of the receptor through two NH…X− and two aromatic CH…X− interactions. The results from solution and theoretical studies suggest that binding is predominately influenced by hydrogen bonding interactions and the basicity of anions.
PMCID: PMC3342016  PMID: 22545400
Urea receptor; Anion coordination; UV-Vis titrations; Host-guest complex; Anion selectivity
6.  Thermodynamic Calculations for Molecules with Asymmetric Internal Rotors. II. Application to the 1,2-Dihaloethanes 
The thermodynamic properties of three halocarbon molecules relevant in atmospheric and public health applications are presented from ab initio calculations. Our technique makes use of a reaction path-like Hamiltonian to couple all the vibrational modes to a large-amplitude torsion for 1,2-difluoroethane, 1,2-dichloroethane, and 1,2-dibromoethane, each of which possesses a heavy asymmetric rotor. Optimized ab initio energies and Hessians were calculated at the CCSD(T) and MP2 levels of theory, respectively. In addition, to investigate the contribution of electronically excited states to thermodynamic properties, several excited singlet and triplet states for each of the halocarbons were computed at the CASSCF/MRCI level. Using the resulting potentials and projected frequencies, the couplings of all the vibrational modes to the large-amplitude torsion are calculated using the new STAR-P 2.4.0 software platform that automatically parallelizes our codes with distributed memory via a familiar MATLAB interface. Utilizing the efficient parallelization scheme of STAR-P, we obtain thermodynamic properties for each of the halocarbons, with temperatures ranging from 298.15 to 1000 K. We propose that the free energies, entropies, and heat capacities obtained from our methods be used to supplement theoretical and experimental values found in current thermodynamic tables.
PMCID: PMC3341731  PMID: 17663439
thermodynamic properties; halocarbons; internal rotation; large-amplitude torsion; vibrations
7.  A C3 Symmetric Nitrate Complex with a Thiophene-Based Tripodal Receptor 
Crystal growth & design  2011;11(4):959-963.
A thiophene-based tripodal receptor has been synthesized and its complexes with nitrate and iodide have determined by single-crystal X-ray analysis. In the nitrate complex, one nitrate is encapsulated in a selective orientation forming a C3 symmetric complex, which is bonded to three protonated secondary amines with six NH···O bonds. The anion is coordinated in a plane perpendicular to the principal rotation axis passing through the tertiary nitrogen of the receptor and the nitrogen of the encapsulated nitrate. High-level DFT calculations support the crystallographic results demonstrating that an adduct with trigonal binding of three oxygen atoms is more stable than that of one oxygen atom of the encapsulate nitrate. On the other hand, in the structure of the iodide complex, all three iodides lie outside the cavity. 1H NMR titration studies indicate that the receptor forms a 1:1 complex with nitrate with a binding constant of K = 315 M−1 in chloroform, showing a moderate selectivity over halides and perchlorate.
PMCID: PMC3086375  PMID: 21552352
8.  Color Detection Using Chromophore-Nanotube Hybrid Devices 
Nano Letters  2009;9(3):1028-1033.
We present a nanoscale color detector based on a single-walled carbon nanotube functionalized with azobenzene chromophores, where the chromophores serve as photoabsorbers and the nanotube as the electronic read-out. By synthesizing chromophores with specific absorption windows in the visible spectrum and anchoring them to the nanotube surface, we demonstrate the controlled detection of visible light of low intensity in narrow ranges of wavelengths. Our measurements suggest that upon photoabsorption, the chromophores isomerize from the ground state trans configuration to the excited state cis configuration, accompanied by a large change in dipole moment, changing the electrostatic environment of the nanotube. All-electron ab initio calculations are used to study the chromophore-nanotube hybrids and show that the chromophores bind strongly to the nanotubes without disturbing the electronic structure of either species. Calculated values of the dipole moments support the notion of dipole changes as the optical detection mechanism.
PMCID: PMC3258674  PMID: 19206226
9.  Formation of an Amine-Water Cyclic Pentamer: A New Type of Water Cluster in a Polyazacryptand 
Crystal growth & design  2010;10(4):1486-1488.
Structural analysis of an adduct of a thiophene-based cryptand with tosylic acid shows the formation of a hybrid amine-water cyclic pentamer composed of four water molecules and one protonated amine in the charged hydrophobic cavity. The bulky tosylate groups remain outside the cavity, making the ligand favorable for hosting water molecules. Ab initio calculations based on density functional theory (DFT) confirm that the hybrid amine-water pentamer is stabilized inside the hydrophobic cavity of the cryptand.
PMCID: PMC2873190  PMID: 20495666
10.  Charge-assisted encapsulation of two chlorides by a hexaprotonated azamacrocycle 
Crystal growth & design  2010;10(4):1478-1781.
A chloride complex of a hexaprotonated azamacrocycle has been isolated, and its structure has been determined by X-ray crystallography showing two encapsulated chloride anions in the cavity. The two internal guests are coordinated at two binding sites on the opposite side of the macrocycle through trigonal recognition by hydrogen-bonding interactions. The other four chlorides are located outside the cavity, each with a single hydrogen bond from secondary amines. Ab initio calculations based on density functional theory (DFT) suggest that the encapsulation of two chlorides inside the cavity leads to a significant charge transfer from the anions to the protonated amines.
PMCID: PMC2873200  PMID: 20495667
11.  Rational design of a macrocyclic-based chemosensor for anions 
Tetrahedron letters  2010;51(9):1329-1332.
A macrocyclic-based fluorescence chemosensor has been designed and synthesized from the reaction of dansyl chloride and a hexaaminomacrocycle containing four secondary and two tertiary amines. The new chemosensor has been examined for its binding ability toward phosphate, sulfate, nitrate, iodide, bromide, chloride, and fluoride by fluorescence spectroscopy in DMSO. The results indicate that the compound binds each of the anions with a 1:1 stoichiometry, showing high affinity for the oxoanions, chloride and iodide with the binding constants up to four orders of magnitude. Ab initio calculations based on density functional theory (DFT) suggest that the ligand is deformed in order to encapsulate an anion, and each anion, except fluoride, is bonded to the macrocycle through two NH…X− and four CH…X− interactions.
PMCID: PMC2855135  PMID: 20401319
12.  (E)-4-[(4-Nitro­phen­yl)diazen­yl]phenyl anthracene-9-carboxyl­ate 
In the title compound, C27H17N3O4, the azo group displays a trans conformation and the dihedral angles between the central benzene ring and the pendant anthracene and nitro­benzene rings are 82.94 (7) and 7.30 (9)°, respectively. In the crystal structure, weak C—H⋯O hydrogen bonds, likely associated with a dipole moment present on the mol­ecule, help to consolidate the packing.
PMCID: PMC2959833  PMID: 21581239
13.  (E)-2-{Eth­yl[4-(4-nitro­phenyl­diazen­yl)phen­yl]amino}ethyl anthracene-9-carboxyl­ate 
The crystal structure of the title compound, C31H26N4O4, displays a trans conformation for the nitro­phenyl­diazenyl portion of the mol­ecule. Packing diagrams indicate that weak C—H⋯O hydrogen bonds, likely associated with a strong dipole moment present in the mol­ecule, dictate the arrangement of mol­ecules in the crystal structure.
PMCID: PMC2960836  PMID: 21201933
14.  Optoelectronic and Excitonic Properties of Oligoacenes: Substantial Improvements from Range-Separated Time-Dependent Density Functional Theory 
The optoelectronic and excitonic properties in a series of linear acenes (naphthalene up to heptacene) are investigated using range-separated methods within time-dependent density functional theory (TDDFT). In these rather simple systems, it is well-known that TDDFT methods using conventional hybrid functionals surprisingly fail in describing the low-lying La and Lb valence states, resulting in large, growing errors for the La state and an incorrect energetic ordering as a function of molecular size. In this work, we demonstrate that the range-separated formalism largely eliminates both of these errors and also provides a consistent description of excitonic properties in these systems. We further demonstrate that reoptimizing the percentage of Hartree−Fock exchange in conventional hybrids to match wave function-based benchmark calculations still yields serious errors, and a full 100% Hartree−Fock range separation is essential for simultaneously describing both of the La and Lb transitions. From an analysis of electron−hole transition density matrices, we finally show that conventional hybrid functionals over-delocalize excitons and underestimate quasiparticle energy gaps in the acene systems. The results of our present study emphasize the importance of both a range-separated and asymptotically correct contribution of exchange in TDDFT for investigating optoelectronic and excitonic properties, even for these simple valence excitations.
PMCID: PMC3002181  PMID: 21170284
15.  Nanoscale Effects on Heterojunction Electron Gases in GaN/AlGaN Core/Shell Nanowires 
Nano Letters  2011;11(8):3074-3079.
The electronic properties of heterojunction electron gases formed in GaN/AlGaN core/shell nanowires with hexagonal and triangular cross sections are studied theoretically. We show that at nanoscale dimensions, the nonpolar hexagonal system exhibits degenerate quasi-one-dimensional electron gases at the hexagon corners, which transition to a core-centered electron gas at lower doping. In contrast, polar triangular core/shell nanowires show either a nondegenerate electron gas on the polar face or a single quasi-one-dimensional electron gas at the corner opposite the polar face, depending on the termination of the polar face. More generally, our results indicate that electron gases in closed nanoscale systems are qualitatively different from their bulk counterparts.
PMCID: PMC3176631  PMID: 21696178
Nanowires; electron gas; polarization; core−shell; heterojunction; AlGaN
16.  Stress Sensing in Polycaprolactone Films via an Embedded Photochromic Compound 
ACS Applied Materials & Interfaces  2010;2(6):1594-1600.
A photochromic polymer exhibiting mechanochromic behavior is prepared by means of ring-opening polymerization (ROP) of ε-caprolactone by utilizing a difunctional indolinospiropyran as an initiator. The configuration of having the photochromic initiating species within the polymer backbone leads to a mechanochromic effect with deformation of polymer films leading to ring-opening of the spiro C−O bond to form the colored merocyanine. Active stress monitoring by dynamic mechanical analysis (DMA) in tension mode was used to probe the effects of UV irradiation on polymer films held under constant strain. Irradiation with UV light induces a negative change in the polymer stress of approximately 50 kPa. Finally, a model of the mechanochromic effect was performed using density functional theory (DFT) and time-dependent DFT (TDDFT) calculations. A sharp increase in the relative molecular energy and the absorption wavelength as well as a drastic decrease in the spiro-oxygen atom charge occurred at a molecular elongation of >39%.
PMCID: PMC3284193  PMID: 20568704
mechanochromic; photochromic; spiropyran; ROP; DFT
17.  Optoelectronic Properties of Carbon Nanorings: Excitonic Effects from Time-Dependent Density Functional Theory 
The electronic structure and size-scaling of optoelectronic properties in cycloparaphenylene carbon nanorings are investigated using time-dependent density functional theory (TDDFT). The TDDFT calculations on these molecular nanostructures indicate that the lowest excitation energy surprisingly becomes larger as the carbon nanoring size is increased, in contradiction with typical quantum confinement effects. In order to understand their unusual electronic properties, I performed an extensive investigation of excitonic effects by analyzing electron-hole transition density matrices and exciton binding energies as a function of size in these nanoring systems. The transition density matrices allow a global view of electronic coherence during an electronic excitation, and the exciton binding energies give a quantitative measure of electron-hole interaction energies in the nanorings. Based on overall trends in exciton binding energies and their spatial delocalization, I find that excitonic effects play a vital role in understanding the unique photoinduced dynamics in these carbon nanoring systems.
PMCID: PMC3317592  PMID: 22481999
18.  Electronic Properties of Vinylene-Linked Heterocyclic Conducting Polymers: Predictive Design and Rational Guidance from DFT Calculations 
The band structure and electronic properties in a series of vinylene-linked heterocyclic conducting polymers are investigated using density functional theory (DFT). In order to accurately calculate electronic band gaps, we utilize hybrid functionals with fully periodic boundary conditions to understand the effect of chemical functionalization on the electronic structure of these materials. The use of predictive first-principles calculations coupled with simple chemical arguments highlights the critical role that aromaticity plays in obtaining a low band gap polymer. Contrary to some approaches which erroneously attempt to lower the band gap by increasing the aromaticity of the polymer backbone, we show that being aromatic (or quinoidal) in itself does not ensure a low band gap. Rather, an iterative approach which destabilizes the ground state of the parent polymer toward the aromatic ↔ quinoidal level crossing on the potential energy surface is a more effective way of lowering the band gap in these conjugated systems. Our results highlight the use of predictive calculations guided by rational chemical intuition for designing low band gap polymers in photovoltaic materials.
PMCID: PMC3334251  PMID: 22540020
19.  Nonempirically Tuned Range-Separated DFT Accurately Predicts Both Fundamental and Excitation Gaps in DNA and RNA Nucleobases 
Using a nonempirically tuned range-separated DFT approach, we study both the quasiparticle properties (HOMO–LUMO fundamental gaps) and excitation energies of DNA and RNA nucleobases (adenine, thymine, cytosine, guanine, and uracil). Our calculations demonstrate that a physically motivated, first-principles tuned DFT approach accurately reproduces results from both experimental benchmarks and more computationally intensive techniques such as many-body GW theory. Furthermore, in the same set of nucleobases, we show that the nonempirical range-separated procedure also leads to significantly improved results for excitation energies compared to conventional DFT methods. The present results emphasize the importance of a nonempirically tuned range-separation approach for accurately predicting both fundamental and excitation gaps in DNA and RNA nucleobases.
PMCID: PMC3419459  PMID: 22904693
20.  An Efficient and Accurate Formalism for the Treatment of Large Amplitude Intramolecular Motion 
We propose a general approach to describe large amplitude motions (LAM) with multiple degrees of freedom (DOF) in molecules or reaction intermediates, which is useful for the computation of thermochemical or kinetic data. The kinetic part of the LAM Lagrangian is derived using a Z-matrix internal coordinate representation within a new numerical procedure. This derivation is exact for a classical system, and the uncertainties on the prediction of observable quantities largely arise from uncertainties on the LAM potential energy surface (PES) itself. In order to rigorously account for these uncertainties, we present an approach based on Bayesian theory to infer a parametrized physical model of the PES using ab initio calculations. This framework allows for quantification of uncertainties associated with a PES model as well as the forward propagation of these uncertainties to the quantity of interest. A selection and generalization of some treatments accounting for the coupling of the LAM with other internal or external DOF are also presented. Finally, we discuss and validate the approach with two applications: the calculation of the partition function of 1,3-butadiene and the calculation of the high-pressure reaction rate of the CH3 + H → CH4 recombination.
PMCID: PMC3419465  PMID: 22904694
21.  Molecular Dynamics Studies of Dislocations in CdTe Crystals from a New Bond Order Potential 
Cd1-xZnxTe (CZT) crystals are the leading semiconductors for radiation detection, but their application is limited by the high cost of detector-grade materials. High crystal costs primarily result from property nonuniformity that causes low manufacturing yield. Although tremendous efforts have been made in the past to reduce Te inclusions/precipitates in CZT, this has not resulted in an anticipated improvement in material property uniformity. Moreover, it is recognized that in addition to Te particles, dislocation cells can also cause electric field perturbations and the associated property nonuniformities. Further improvement of the material, therefore, requires that dislocations in CZT crystals be understood and controlled. Here, we use a recently developed CZT bond order potential to perform representative molecular dynamics simulations to study configurations, energies, and mobilities of 29 different types of possible dislocations in CdTe (i.e., x = 1) crystals. An efficient method to derive activation free energies and activation volumes of thermally activated dislocation motion will be explored. Our focus gives insight into understanding important dislocations in the material and gives guidance toward experimental efforts for improving dislocation network structures in CZT crystals.
PMCID: PMC3433129  PMID: 22962626
22.  Thermochemistry of Alane Complexes for Hydrogen Storage: A Theoretical and Experimental Investigation 
Knowledge of the relative stabilities of alane (AlH3) complexes with electron donors is essential for identifying hydrogen storage materials for vehicular applications that can be regenerated by off-board methods; however, almost no thermodynamic data are available to make this assessment. To fill this gap, we employed the G4(MP2) method to determine heats of formation, entropies, and Gibbs free energies of formation for 38 alane complexes with NH3−nRn (R = Me, Et; n = 0−3), pyridine, pyrazine, triethylenediamine (TEDA), quinuclidine, OH2−nRn (R = Me, Et; n = 0−2), dioxane, and tetrahydrofuran (THF). Monomer, bis, and selected dimer complex geometries were considered. Using these data, we computed the thermodynamics of the key formation and dehydrogenation reactions that would occur during hydrogen delivery and alane regeneration, from which trends in complex stability were identified. These predictions were tested by synthesizing six amine−alane complexes involving trimethylamine, triethylamine, dimethylethylamine, TEDA, quinuclidine, and hexamine and obtaining upper limits of ΔG° for their formation from metallic aluminum. Combining these computational and experimental results, we establish a criterion for complex stability relevant to hydrogen storage that can be used to assess potential ligands prior to attempting synthesis of the alane complex. On the basis of this, we conclude that only a subset of the tertiary amine complexes considered and none of the ether complexes can be successfully formed by direct reaction with aluminum and regenerated in an alane-based hydrogen storage system.
PMCID: PMC3433776  PMID: 22962624
23.  Comparison of Molecular Dynamics with Classical Density Functional and Poisson–Boltzmann Theories of the Electric Double Layer in Nanochannels 
Comparisons are made among Molecular Dynamics (MD), Classical Density Functional Theory (c-DFT), and Poisson–Boltzmann (PB) modeling of the electric double layer (EDL) for the nonprimitive three component model (3CM) in which the two ion species and solvent molecules are all of finite size. Unlike previous comparisons between c-DFT and Monte Carlo (MC), the present 3CM incorporates Lennard-Jones interactions rather than hard-sphere and hard-wall repulsions. c-DFT and MD results are compared over normalized surface charges ranging from 0.2 to 1.75 and bulk ion concentrations from 10 mM to 1 M. Agreement between the two, assessed by electric surface potential and ion density profiles, is found to be quite good. Wall potentials predicted by PB begin to depart significantly from c-DFT and MD for charge densities exceeding 0.3. Successive layers are observed to charge in a sequential manner such that the solvent becomes fully excluded from each layer before the onset of the next layer. Ultimately, this layer filling phenomenon results in fluid structures, Debye lengths, and electric surface potentials vastly different from the classical PB predictions.
PMCID: PMC3542913  PMID: 23316120

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