3‑Input AND Molecular Logic Gate with Enhanced Fluorescence Output: The Key Atom for the Accurate Prediction of the Spectra

The development of artificial receptors for sensing and recognition of species, as well as for advanced logic functions, is a significant challenge in the field of molecular information technology. Here, we study theoretically, via DFT/TD-DFT calculations, the photophysical properties of a 3-input AND molecular logic gate which presents an enhanced fluorescence spectrum. It was found that the geometry conformation at an N atom of the piperazine group is the key factor for the correct calculation of the absorption spectra of the calculated structures. Its geometry is between tetrahedral and planar, while changes in the corresponding CNCC dihedral angle of about 10 degrees can cause significant shifts of the main peak of the absorption spectra up to 100 nm. Moreover, the unusually enhanced fluorescence of a molecular logic gate (MLG) is explained. Finally, we conclude that molecular systems having N atoms, whose geometry is between planar and tetrahedral, can be ideal molecules as sensors and molecular logic gates. Our calculated absorption and emission spectra are in excellent agreement with available experimental data

Theoretical Investigation on the Electronic and Geometric Structure of GaN₂⁺ and GaN₄⁺

The electronic and geometric structures of gallium dinitride cation, GaN2+ and gallium tetranitride cation, GaN4+ were systematically studied by employing density functional theory (DFT-B3LYP) and perturbation theory (MP2, MP4) in conjunction with large basis sets, (aug-)cc-pVxZ, x = T, Q. A total of 7 structures for GaN2+ and 24 for GaN4+ were identified, corresponding to minima, transition states, and saddle points. We report geometries and dissociation energies for all the above structures as well as potential energy profiles, potential energy surfaces, and bonding mechanisms for some low-lying electronic states. The calculated dissociation energy (De) of the ground state of GaN2+, X̃Σ+, is 5.6 kcal/mol with respect to Ga+(1S) + N2(X1Σg+) and that of the excited state, ã3Π, is 24.8 kcal/mol with respect to Ga+(3P) + N2(X1Σg+). The ground state and the first excited minimum of GaN4+ are of 1A1(C2v) and 3B1(C2v) symmetry with corresponding De of 11.0 and 43.7 kcal/mol with respect to Ga+(1S) + 2N2(X1Σg+) for X1A1 and Ga+(3P) + 2N2(X1Σg+) for 3B1

Theoretical Study of Adsorption and Diffusion of Group IIIA Metals on Si(111)

Adsorption of group IIIA elements (M = B, Al, Ga, and In) on a model Si(111) surface was studied by density functional theory calculations. Eight stable structures were determined for the M adsorbed species. The incorporation of the M atoms on the Si surface is investigated, and the energy barriers for the incorporation are calculated. The binding energy of the lowest calculated minimum of chemisorbed M at Si(111), after correcting for the basis set superposition error, is 6.3 (B, S5 substitutional site), 3.4 (Al, T4 adsorption site), 2.9 (Ga, T4), and 2.5 (In, T4) eV. Our results are in good agreement with previous experimental work, where available. The activation energy barrier from the T4 to the H3 adsorption site is 1.2 (Al), 1.1 (Ga), and 0.7 eV (In); the activation energy barrier from the lowest energy structure with M connected to the surface at a dangling bond to a precursor of T4 is 0.5 (B), 1.6 (Al), 1.7 (Ga), and 1.9 eV (In)

First Principles Examination of the Acetylene−Water Clusters, HCCH−(H₂O)<i>_x</i>, <i>x </i>= 2, 3, and 4

The acetylene−water (A−W) interactions have been investigated by examining the van der Waals clusters AWx, x = 2, 3, and 4, at the second order (MP2) perturbation theory using the correlation-consistent basis sets, aug-cc-pVnZ, n = D (AW2, AW3, and AW4), T (AW2). We located 4 minima (m) and 2 saddle points (sp), 10 m and 3 sp, and 30 m and 3 sp on the potential energy surfaces of the AW2, AW3, and AW4 clusters, respectively. We report the fully optimized geometries and interaction energies ΔEe, including corrections for basis set superposition error, ΔEe(BSSE), as well as zero-point energies, ΔE0(BSSE), for the various stationary points. The global minima of the AW2 and AW3 clusters are cyclic configurations in which the acetylene molecule inserts into the water hydrogen bonding network. The corresponding interaction energies ΔEe(BSSE)[ΔE0(BSSE)] are AW2, −10.37 [−6.70] kcal/mol (MP2/aug-cc-pVTZ) and AW3, −17.80 [−11.46] kcal/mol (MP2/aug-cc-pVDZ). The global minimum of AW4 corresponds to a van der Waals complex between a cyclic water tetramer W4 and A with an interaction energy of −28.01 [−18.67] kcal/mol (MP2/aug-cc-pVDZ). The 4 and 10 local minima for the x = 2 and 3 clusters span an energy range of 4.3 and 6.1 kcal/mol above the respective global minima. For AW4, the energy range for the 30 minima is 14.1 kcal/mol; however, the first 28 lie within 8.4 kcal/mol above the global minimum. The analysis of the many-body interaction energy terms suggests that the global and low-lying ring networks are stabilized by the maximization of the many-body (mainly the 3-body) terms, whereas the higher lying minima are mainly described by 2-body interactions

Computational Insight into the Electronic Structure and Absorption Spectra of Lithium Complexes of N-Confused Tetraphenylporphyrin

The present work is a theoretical investigation on lithium complexes of N-confused tetraphenylporphyrins (aka inverted) employing density functional theory (DFT) and time-dependent DFT, using the B3LYP, CAM-B3LYP, and M06-2X functionals in conjunction with the 6-31G(d,p) basis set. The purpose of the present study is to calculate the electronic structure and the bonding of the complexes to explain the unusual coordination environment in which Li is found experimentally and how the Li binding affects the Q and the Soret bands. The calculations show that, unlike a typical tetrahedral Li+ cation, this Li forms a typical bond with one N and interacts with the remaining two N atoms, and it is located in the right place to form an agostic-like interaction with the internal C atom. The reaction energy, the enthalpy for the formation of the lithium complexes of N-confused porphyrins, and the effect of solvation are also calculated. The insertion of Li into N-confused porphyrin, in the presence of tetrahydrofuran, is exothermic with a reaction energy calculated to be as high as −72.4 kcal/mol using the lithium bis(trimethylsilyl)amide reagent. Finally, there is agreement in the general shape among the vis–UV spectra determined with different functionals and the experimentally available ones. The calculated geometries are in agreement with crystallographic data, where available

Theoretical Study of Gallium Nitride Molecules, GaN₂ and GaN₄.

The electronic and geometric structures of gallium dinitride GaN2, and gallium tetranitride molecules, GaN4, were systematically studied by employing density functional theory and perturbation theory (MP2, MP4) in conjunction with the aug-cc-pVTZ basis set. In addition, for the ground-state of GaN4(2B1) a density functional theory study was carried out combining different functionals with different basis sets. A total of 7 minima have been identified for GaN2, while 37 structures were identified for GaN4 corresponding to minima, transition states, and saddle points. We report geometries and dissociation energies for all the above structures as well as potential energy profiles, potential energy surfaces and bonding mechanisms for some low-lying electronic states of GaN4. The dissociation energy of the ground-state GaN2 (X̃2Π) is 1.1 kcal/mol with respect to Ga(2P) + N2(X1Σg+). The ground-state and the first two excited minima of GaN4 are of 2B1(C2v), 2A1(C2v, five member ring), and 4Σg−(D∞h) symmetry, respectively. The dissociation energy (De) of the ground-state of GaN4, X̃2B1, with respect to Ga(2P) + 2 N2(X1Σg+), is 2.4 kcal/mol, whereas the De of 4Σg− with respect to Ga(4P) + 2 N2(X1Σg+) is 17.6 kcal/mol

Quantitative Account of the Bonding Properties of a Rubredoxin Model Complex [Fe(SCH₃)₄]^<i>q</i>, <i>q</i> = −2, −1, +2, +3

Iron–sulfur clusters play important roles in biology as parts of electron-transfer chains and catalytic cofactors. Here, we report a detailed computational analysis of a structural model of the simplest natural iron–sulfur cluster of rubredoxin and its cationic counterparts. Specifically, we investigated adiabatic reduction energies, dissociation energies, and bonding properties of the low-lying electronic states of the complexes [Fe­(SCH3)4]2–/1–/2+/3+ using multireference (CASSCF, MRCISD), and coupled cluster [CCSD­(T)] methodologies. We show that the nature of the Fe–S chemical bond and the magnitude of the ionization potentials in the anionic and cationic [Fe­(SCH3)4] complexes offer a physical rationale for the relative stabilization, structure, and speciation of these complexes. Anionic and cationic complexes present different types of chemical bonds: prevalently ionic in [Fe­(SCH3)4]2–/1– complexes and covalent in [Fe­(SCH3)4]2+/3+ complexes. The ionic bonds result in an energy gain for the transition [Fe­(SCH3)4]2– → [Fe­(SCH3)4]− (i.e., FeII → FeIII) of 1.5 eV, while the covalent bonds result in an energy loss for the transition [Fe­(SCH3)4]2+ → [Fe­(SCH3)4]3+ of 16.6 eV, almost half of the ionization potential of Fe2+. The ionic versus covalent bond character influences the Fe–S bond strength and length, that is, ionic Fe–S bonds are longer than covalent ones by about 0.2 Å (for FeII) and 0.04 Å (for FeII). Finally, the average Fe–S heterolytic bond strength is 6.7 eV (FeII) and 14.6 eV (FeIII) at the RCCSD­(T) level of theory

Theoretical Study of Hydrogen Bonding in Homodimers and Heterodimers of Amide, Boronic Acid, and Carboxylic Acid, Free and in Encapsulation Complexes

The homodimers and the heterodimers of two amides, two boronic acids, and two carboxylic acids have been calculated in the gas phase and in N,N-dimethylformamide (DMF) and CCl4 solvents using the DFT (M06-2X and M06-L) and the MP2 methods in conjunction with the 6-31G(d,p) and 6-311+G(d,p) basis sets. Furthermore, their pairwise coencapsulation was studied to examine its effect on the calculated properties of the hydrogen bonds at the ONIOM[M06-2X/6-31G(d,p);PM6], ONIOM[MP2/6-31G(d,p); PM6], and M06-2X/6-31G(d,p) levels of theory. The present work is directed toward the theoretical rationalization and interpretation of recent experimental results on hydrogen bonding in encaptulation complexes [D. Ajami et al. J. Am. Chem. Soc. 2011, 133, 9689–9691]. The calculated dimerization energy (ΔE) values range from 0.74 to 0.35 eV for the different dimers in the gas phase, with the ordering carboxylic homodimers > amide-carboxylic dimers > amide homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic homodimers. In solvents, generally smaller ΔE values are calculated with only small variations in the ordering. In the capsule, the ΔE values range between 0.67 and 0.33 eV with practically the same ordering as in the gas phase. The calculated % distributions of the encapsulated dimers, taking into account statistical factors, are in agreement with the experimental distribution, where the occurrence of boronic homodimer dominates, even though it is calculated to have the smallest ΔE

Conformations and Fluorescence of Encapsulated Stilbene

Absorption and emission spectra of free and encapsulated stilbene in two different capsules were calculated using the DFT and the TDDFT methodology at the B3LYP, CAM-B3LYP, M06-2X, PBE0, and ωB97X-D/6-31G­(d,p) levels of theory. The present work is directed toward the theoretical interpretation of recent experimental results on control of stilbene conformation and fluorescence in capsules [Ams, M. R.; et al. <i>Beilstein J. Org. Chem.</i> <b>2009</b>, <i>5</i>, 79]. The results of the calculations are in agreement with experiment and show that fluorescence of <i>trans</i>-stilbene persists in the large cage while it is quenched in the small one. It is found that the geometry of <i>trans</i>-stilbene in the ground as well as in the first excited singlet state is unaffected by encapsulation in the large cage, and consequently the absorption and emission spectra are similarly unaffected. In the small cage, the ground state of encapsulated <i>trans</i>-stilbene is distorted, with the two phenyl groups twisted, while the geometry of the excited state, after relaxation, lies at the conical intersection with the ground state. Consequently, there is no emission similar to that of free <i>trans</i>-stilbene, and the state decays nonradiatively to the ground state

Molybdenum–Sulfur Bond: Electronic Structure of Low-Lying States of MoS

The molybdenum–sulfur bond plays an important role in many processes such as nitrogen-fixation, and it is found as a building block in layered materials such as MoS2, known for its various shapes and morphologies. Here, we present an accurate theoretical and experimental investigation of the chemical bonding and the electronic structure of 20 low-lying states of the MoS molecule. Multireference and coupled cluster methodologies, namely, MRCISD, MRCISD + Q, RCCSD­(T), and RCCSD­[T], were employed in conjunction with basis sets up to aug-cc-pwCV5Z-PP/aug-cc-pwCV5Z for the study of these states. We note the significance of including the inner 4s24p6 electrons of Mo and 2s22p6 of S in the correlated space to obtain accurate results. Experimentally, the predissociation threshold of MoS was measured using resonant two-photon ionization spectroscopy, allowing for a precise measurement of the bond dissociation energy. Our extrapolated computational D0 value for the ground state is 3.936 eV, in excellent agreement with our experimental measurement of 3.932 ± 0.004 eV. The largest calculated adiabatic D0 (5.74 eV) and the largest dipole moment (6.50 D) were found for the 5Σ+ state, where a triple bond is formed. Finally, the connection of the chemical bonding of the isolated MoS species to the relevant solid, MoS2, is emphasized. The low-lying septet states of the diatomic molecule are involved in the material as a building block, explaining the stability and the variety of the shapes and morphologies of the material