The Effect of Intermolecular Hydrogen Bonding on the Polyaniline Water Complex

The polyaniline water hydrogen-bonded complex was studied by first-principles calculation. The density functional theory method was used to calculate the structure characters, natural bond orbital charge distribution, infrared spectra and the frontier molecular orbital. Results showed that the H–O···H–N and C–N···H–O type intermolecular hydrogen bonds were formed. The bonds involved in the intermolecular H-bond were all influenced by the hydrogen bonding interaction. During the hydrogen bond formation, the polymer chains in the complexes were all charged, which can be an important factor contributing to the increase of electrical conductivity. The N1–H vibration was strongly influenced, and the locations as well as the intensities of N1–H absorption bands were all changed in the complexes. In the orbital transition of HOMO to LUMO, the electron density transferred from benzenoid ring to quinoid ring.     

Molecular design of a π‐conjugated single‐chain electronically conductive polymer

This study demonstrates that single‐chain π‐conjugated systems can be made electrically conductive by modifying the molecular structures of both ends of the oligomers making up a polymer. That is, the highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gaps of a fairly long polyyne‐type oligomer with appropriately modified molecular structures at both ends are found to be on the order of thermal energy by calculations using density functional theory (DFT) with B3LYP functionals. This result applies to molecular structures with characteristic bond alternations. The peculiar bond alternations are caused by competition between two effects of the bond alternations of the two mutually perpendicular π‐conjugated systems, which partially cancel each other out. It is probable that we can design one‐dimensional polymers with HOMO–LUMO gaps small enough to be conductive by combining the above‐mentioned oligomers with each other as monomer units in the polymer. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical and experimental studies on solubility and reactivity behavior of lysergol,elymoclavine, and dihydrolysergol

Lysergol, elymoclavine (Δ^9,10 and Δ^8,9 regioisomers), and dihydrolysergol are important members of ergolines. The present work reports their comparative study in gas and solvent phase (water) that has been performed both experimentally and theoretically. Theortical calculations have been carried within the density functional theory formalism to analyze the structural and electronic properties of these molecules with B3LYP hybrid exchange–correlational fuctional in conjunction with 6‐311++G (d,p) basis set. Hessian calculations are performed at B3LYP/6‐31G (d,p) level of theory in gas phase as well as other solvent phases. Solvent phase calculations are performed using Onsager reaction field model as implemented in Gaussian 03. A good agreement has been found between experimental and theoretical infrared and nuclear magnetic resonance (NMR) spectra. The calculated NMR data has been analyzed statistically. Stability of these regioisomers has been analyzed in terms of the energy gap between highest occupied molecular orbital and lowest unoccupied molecular orbital (HOMO–LUMO gap). Calculations for lysergol and elymoclavine in water as solvent were carried to examine the effect of solvent on the HOMO–LUMO levels and energy of these molecules. © 2012 Wiley Periodicals, Inc.     

Comparative study of the electronic structure of pregnanolones by ab initio theory

Pregnanedione (5β‐pregnane, 3,20‐dione), pregnanolone (3β‐hydroxy‐5β‐pregnan‐20‐one), and epipregnanolone (3α‐hydroxy‐5β‐pregnan‐20‐one) result from the 5β‐reduction of progesterone [4‐pregnene, 3‐20‐dione (P)]. These P metabolites induce anesthesia and smooth muscle relaxation (nongenomic actions). In the present study, geometries and electronic structure of these steroids were assessed by ab initio calculations using the 6‐31G* basis set. Consequently, bond distances, valence angles, and dihedral angles were measured. In addition total energy, frontier orbitals, i.e., highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), dipole moment, and electrostatic potentials were calculated. Total energy was higher for P, followed by pregnanedione. Pregnanolones, the hydroxylated progestins, showed the lower energies. Concerning frontier orbitals, P showed the highest HOMO energy and the lowest LUMO energy. Pregnanedione showed lower HOMO and LUMO energy values than pregnanolone and epipregnanolone. P showed both HOMO and LUMO located at the A ring, including the π bond at C4, C5, and the carbonyl at C3. The HOMO in pregnanedione was included mostly in the A ring and the C3 carbonyl group, while the LUMO was shared by the carbonyl groups at C3 and C20. The frontier orbitals of pregnanolone and epipregnanolone were quite similar. The HOMO in both steroids included the B, C, and D rings and the carbonyl at C20. The LUMO was also similar in both pregnanolones including mostly the carbonyl at C20. The dipole moment was shorter for P and pregnanedione and directed toward the acetyl side chain at C17. Pregnanolone and epipregnanolone showed the dipole moment vector larger and directed toward the A ring. The electrostatic potentials were related mostly with the lone pairs of electrons from the oxygens. By the total energy and frontier orbitals energies of the hormones studied, it is concluded that the metabolism of progesterone toward its 5β‐reduced metabolites might be rationalized from the theoretical chemistry point of view. Besides, the importance of the A/B ring cis configuration, dipole moment, and electrostatic potential are highlighted as possible improving elements of molecular interactions to explain the nongenomic biological action of 5β‐reduced progestins. ©1999 John Wiley & Sons, Inc. Int J Quant Chem 71: 433–440, 1999     

4‐(3,5‐Dimethyl‐1H‐pyrazol‐4‐ylmethyl)‐3,5‐dimethyl‐1H‐pyrazol‐2‐ium dihydrogen phosphate: a combined X‐ray and DFT study

The molecular structure of the title salt, C₁₁H₁₇N₄⁺·H₂PO₄⁻, has been determined from single‐crystal X‐ray analysis and compared with the structure calculated by density functional theory (DFT) at the BLYP level. The crystal packing in the title compound is stabilized primarily by intermolecular N—H...O, O—H...N and O—H...O hydrogen bonds and π–π stacking interactions, and thus a three‐dimensional supramolecular honeycomb network consisting of R₄²(10), R₄⁴(14) and R₄⁴(24) ring motifs is established. The HOMO–LUMO energy gap (1.338 eV; HOMO is the highest occupied molecular orbital and LUMO is the lowest unoccupied molecular orbital) indicates a high chemical reactivity for the title compound.     

Electronic and Chemical Characterization of Aluminum–Nitrogen (AlN) Substituted Fullerenes: C58AlN to C24Al12N12

Density functional theory calculations (B3LYP/6-311G*) are applied to devise a series of AlN-substituted C₆₀ fullerenes, avoiding weak homonuclear Al–Al and N–N bonds. The substitutional structures, energy gaps between the highest occupied molecular orbital and the lowest unoccupied molecular orbital, ionization potentials, binding energies, as well as dipole moments have been systematically investigated. The band gap (HOMO–LUMO gap) is larger for all the AlN-substituted fullerenes than C₆₀. The properties of heterofullerenes, especially, the HOMO–LUMO strongly depend on the number of AlN units. Natural charge analyses indicate that doping of fullerene with AlN units exerts electronic environment diversity to the cage. High charge transfer on the surfaces of our heterofullerenes provokes more studies on their possible application for hydrogen storage.     

Optical properties of (Z)‐2‐(2‐phenylhydrazinylidene)acenaphthen‐1(2H)‐one: a potential electron donor in organic solar cells

Electron‐donating molecules play an important role in the development of organic solar cells. (Z )‐2‐(2‐Phenylhydrazinylidene)acenaphthen‐1(2H )‐one (PDAK), C₁₈H₁₂N₂O, was synthesized by a Schiff base reaction. The crystal structure shows that the molecules are planar and are linked together forming `face‐to‐face' assemblies held together by intermolecular C—H…O, π–π and C—H…π interactions. PDAK exhibits a broadband UV–Vis absorption (200–648 nm) and a low HOMO–LUMO energy gap (1.91 eV; HOMO is the highest occupied molecular orbital and LUMO is the lowest unoccupied molecular orbital), while fluorescence quenching experiments provide evidence for electron transfer from the excited state of PDAK to C₆₀. This suggests that the title molecule may be a suitable donor for use in organic solar cells.     

Tuning of the electronic properties of H‐passivated armchair graphene nanoribbons by mild border oxidation: Theoretical study on periodic models

We report the results of a DFT study of the electronic properties, intended as highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies, of periodic models of H‐passivated armchair graphene nanoribbons (a‐GNRs) as that synthetized by bottom‐up technique, functionalized by vicinal dialdehydic groups. This material can be obtained by border oxidation in mild and easy to control conditions with ¹Δ_g O₂ as we reported in our previous paper (Ghigo et al., ChemPhysChem 2015, 16, 3030). The calculations show that the two models of border oxidized a‐GNRs (model A, 0.98 nm and model B, 1.35 nm wide) present LUMO and HOMO energies lowered by an extend roughly linearly dependent on the amount of oxygen chemically bound. The frontier orbital energy variations dependence on the % wt of oxygen bound are, for model A: ?0.12 eV for the LUMO and ?0.05 eV for the HOMO; for model B: ?0.15 eV (HOMO) and ?0.06 eV (LUMO). © 2016 Wiley Periodicals, Inc.     

A Triphenylamine with Two Phenoxy Radicals Having Unusual Bonding Patterns and a Closed‐Shell Electronic State

Reported herein is the structure and the electronic properties of a novel triphenylamine derivative having two phenoxy radicals appended to the amino nitrogen atom. X‐ray single crystal analysis and the magnetic resonance measurements demonstrates the unexpected closed‐shell electronic structure, even at room temperature, of the molecule and two unusual C? N bonds with multiple‐bond character. The theoretical calculations support the experimentally determined molecular geometry with the closed‐shell electronic structure, and predicted a small HOMO–LUMO gap originating from the nonbonding character of the HOMO. The optical and electrochemical measurements show that the molecule has a remarkably small HOMO–LUMO gap compared with its triphenylamine precursor.     

The Pi‐Nature of Methyl Obtained by the Natural Bond Orbital Method: Orbital‐Based Rationalizations of Site‐Dependent Substitution Effects on Fine Color‐Tuning of Luminescence

Both C‐H bonding and antibonding (σ_CH and σ*_CH) of a methyl group would contribute to the highest occupied or lowest unoccupied molecular orbitals (HOMO or LUMO) in methylated derivatives of Ir(ppz)₂ 3 iq (ppz = 1‐phenylpyrazole and 3iq = isoquinoline‐3‐carboxylate). This is found by analysis of HOMO (or LUMO) formed by linear combination of bond orbitals using the natural bond orbital (NBO) method. The elevated level of HOMO (or LUMO) uniformly found for each methylated derivative, indicating the σ_CH‐destabilization outweighs the σ*_CH‐stabilization. To broaden the HOMO‐LUMO gap, methylation at a carbon having smaller contribution to HOMO and/or larger contribution to LUMO is suggested.     

The effect of conjugated spacer on novel carbazole derivatives for dye‐sensitized solar cells: Density functional theory/time‐dependent density functional theory study

The ground‐state structure and frontier molecular orbital of D‐π‐A organic dyes, CFT1A, CFT2A, and CFT1PA were theoretically investigated using density functional theory (DFT) on B3LYP functional with 6‐31G(d,p) basis set. The vertical excitation energies and absorption spectra were obtained using time‐dependent DFT (TD‐DFT). The adsorptions of these dyes on TiO₂ anatase (101) were carried out by using a 38[TiO₂] cluster model using Perdew–Burke–Ernzerhof functional with the double numerical basis set with polarization (DNP). The results showed that the introduction of thiophene–thiophene unit (T–T) as conjugated spacer in CFT2A could affect the performance of intramolecular charge transfer significantly due to the inter‐ring torsion of T–T being decreased compared with phenylene–phenylene (P–P) spacer of CFP2A in the researhcers' previous report. It was also found that increasing the number of π‐conjugated unit gradually enhanced charge separation between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of these dyes, leading to a high‐efficiency photocurrent generation. The HOMO–LUMO energy gaps were calculated to be 2.51, 2.37, and 2.50 eV for CFT1A, CFT2A, and CFT1PA respectively. Moreover, the calculated adsorption energies of these dyes on TiO₂ cluster were ～14 kcal/mol, implying that these dyes strongly bind to TiO₂ surface. Furthermore, the electronic HOMO and LUMO shapes of all dye–TiO₂ complexes exhibited injection mechanism of electron via intermolecular charge‐transfer transition. © 2012 Wiley Periodicals, Inc.     

Hydrogen-bond-induced quantum interference in single-molecule junctions of regioisomers

Solvents can play a significant role in tuning the electrical conductance of single-molecule junctions. In this respect, protic solvents offer the potential to form hydrogen bonds with molecular backbones and induce electrostatic gating via their dipole moments. Here we demonstrate that the effect of hydrogen bond formation on conductance depends on whether transport through the junction is controlled by destructive quantum interference (DQI) or constructive quantum interference (CQI). Furthermore, we show that a protic solvent can be used to switch the conductance of single-molecule junctions between the two forms of quantum interference. To explore this possibility, two regioisomers (BIT-Zwitterion and BIT-Neutral) were synthesized and their single-molecule conductances in aprotic and protic solvents were investigated using a scanning-tunneling-microscope-based break junction technique, combined with density functional theory and quantum transport theory. We find that the protic solvent twists the geometry of BIT-Zwitterion by introducing intermolecular hydrogen bonds between the solvent and target molecule. Moreover, it increases the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the molecule by imposing different electrostatic gating on the delocalized HOMO and localized LUMO, leading to a lower conductance compared to that in aprotic solvent. In contrast, the conductance of BIT-Neutral increases due to a transformation from DQI to CQI originating from a change from a planar to a folded conformation in the protic solvent. In addition, the stacking between the two folded moieties produces an extra through-space transport path, which further contributes to conductance. This study demonstrates that combinations of protic solvents and regioisomers present a versatile route to controlling quantum interference and therefore single-molecule conductance, by enabling control of hydrogen bond formation, electrostatic gating and through-space transport.

We demonstrate that the effect of solvent–molecule interaction through hydrogen bonding on junction conductance depends on whether transport through the junction is controlled by destructive or constructive quantum interference.     

Zeolite-Y entrapped bivalent transition metal complexes as hybrid nanocatalysts: density functional theory investigation and catalytic aspects

The intriguing research toward the exploitation of zeolite-Y-based hybrid nanocatalysts for catalytic oxidation reactions has been growing significantly. In the present investigation, we describe the synthesis of zeolite-Y entrapped transition metal complexes of the general formulae [M(SFCH)·xH₂O]-Y (where, M = Mn, Fe, Co, Ni (x = 3) and Cu (x = 1)); H₂SFCH = (E)-N′-(2-hydroxybenzylidene)furan-2-carbohydrazide]. These nanocatalysts have been characterized by various physicochemical techniques. Density functional theory calculations are performed to address the relaxed geometry, bond angle, bond length, dihedral angle, highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) energy gap, and electronic density of states of H₂SFCH ligand and their neat transition metal complexes. The observed HOMO–LUMO gap and the Fermi energy is higher for Cu(II) complexes, which demonstrates the better catalytic activity of this nanocatalyst. The catalytic activity was performed in liquid-phase oxidation of cyclohexane using hydrogen peroxide as oxidant to give cyclohexanone (CyONE) and cyclohexanol (CyOL). Among them, [Cu(SFCH)·H₂O]-Y catalyst has the highest selectivity toward CyONE (84.5%).     

Mechanistic Analysis of Fluorescence Quenching of Reduced Nicotinamide Adenine Dinucleotide by Oxamate in Lactate Dehydrogenase Ternary Complexes

Fluorescence of Reduced Nicotinamide Adenine Dinucleotide (NADH) is extensively employed in studies of oxidoreductases. A substantial amount of static and kinetic work has focused on the binding of pyruvate or substrate mimic oxamate to the binary complex of lactate dehydrogenase (LDH)‐NADH where substantial fluorescence quenching is typically observed. However, the quenching mechanism is not well understood limiting structural interpretation. Based on time‐dependent density functional theory (TDDFT) computations with cam‐B3LYP functional in conjunction with the analysis of previous experimental results, we propose that bound oxamate acts as an electron acceptor in the quenching of fluorescence of NADH in the ternary complex, where a charge transfer (CT) state characterized by excitation from the highest occupied molecular orbital (HOMO) of the nicotinamide moiety of NADH to the lowest unoccupied molecular orbital (LUMO) of oxamate exists close to the locally excited (LE) state involving only the nicotinamide moiety. Efficient quenching in the encounter complex like in pig heart LDH requires that oxamate forms a salt bridge with Arg‐171 and hydrogen bonds with His‐195, Thr‐246 and Asn‐140. Further structural rearrangement and loop closure, which also brings about another hydrogen bond between oxamate and Arg‐109, will increase the rate of fluorescence quenching as well.     

Density functional study of structural and electronic properties of AlnN (1 ≤ n ≤ 12) clusters

Low‐lying equilibrium geometric structures of Al_nN (n = 1–12) clusters obtained by an all‐electron linear combination of atomic orbital approach, within spin‐polarized density functional theory, are reported. The binding energy, dissociation energy, and stability of these clusters are studied within the local spin density approximation (LSDA) and the three‐parameter hybrid generalized gradient approximation (GGA) due to Becke–Lee–Yang–Parr (B3LYP). Ionization potentials, electron affinities, hardness, and static dipole polarizabilities are calculated for the ground‐state structures within the GGA. It is observed that symmetric structures with the nitrogen atom occupying the internal position are lowest‐energy geometries. Generalized gradient approximation extends bond lengths as compared with the LSDA lengths. The odd–even oscillations in the dissociation energy, the second differences in energy, the highest occupied molecular orbital–lowest unoccupied molecular orbital (HOMO–LUMO) gaps, the ionization potential, the electron affinity, and the hardness are more pronounced within the GGA. The stability analysis based on the energies clearly shows the Al₇N cluster to be endowed with special stability. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Luminescent copoly(aryl ether)s with new electron‐transporting bis(3‐(trifluoromethyl)phenyl)‐1,3,4‐oxadiazole or bis(3‐(trifluoromethyl)phenyl)‐4‐(4‐hexyloxyphenyl)‐4H‐1,2,4‐triazole segments

To investigate the effect of trifluoromethyl groups in enhancing electron affinity of aromatic oxadiazole and triazole chromophores, we prepared four new copoly(aryl ether)s ( P1 – P4 ) consisting of bis(3‐(trifluoromethyl) phenyl)‐1,3,4‐oxadiazole (ETO) or bis(3‐(trifluoromethyl)phenyl)‐4‐(4‐hexyloxyphenyl)‐4H‐1,2,4‐triazole (ETT) segments and hole‐transporting segments [2,5‐distyrylbenzene (HTB) or bis(styryl)fluorine (HTF)]. Molecular spectra (absorption and photoluminescence) and cyclic voltammetry were used to investigate their optical and electrochemical properties. The emissions of P1 – P4 are dominated by the hole‐transporting fluorophores with longer emissive wavelengths around 442–453 nm via efficient excitation energy transfer. The highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy levels of P1 – P4 , estimated from electrochemical data, are ?5.15, ?5.18, ?5.30, ?5.27, ?3.39, ?3.49, ?3.36, and ?3.48 eV, respectively. The LUMO levels of ETO and ETT segments are significantly reduced to ?3.39～?3.36 eV and ?3.48～?3.49 eV, respectively, as compared with ?2.45 eV of P5 containing a 2,5‐diphenyl‐1,3,4‐oxadiazole segment. Moreover, electron and hole affinity can be enhanced simultaneously by introducing isolated hole‐ and electron‐transporting segments in the backbone. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 5900–5910, 2004     

Theoretical Studies on the Mechanistic Insertions of Singlet Methylene and Halomethylene into Polar S‒H Bonds of Methanethiol,Ethanethiol, 1-Propanethiol and 2-Propanethiol

Abstract

The insertion of ¹CH₂, ¹CHF, ¹CF₂,¹CHCl, and ¹CCl₂ into primary and secondary polar S?H bonds of methanethiol, ethanethiol, 1-propanethiol, and 2-propanethiol have been investigated at HF (Hartree–Fock), MP2 (Møller–Plesset Perturbation Theory), and DFT (density functional theory) levels using 6-31G (d, p) basis set. The insertions follow a two-step mechanism. The potential energy surface exploration identifies ylide-like structures undergoing the 1,2-sigmatropic hydrogen shift concertedly giving the thioether product. But ¹CF₂ forms weak complexes involving 1,2-hydrogen shift. The barrier height in the concerted mechanism varies with the type of carbene moiety and S?H bond. The initial interaction seems to be a function of HOMO (highest occupied molecular orbital) and LUMO (lowest unoccupied molecular orbital) energies of thiols and carbenes, respectively. The natural bond orbital charge analysis showing a net charge flow from the substrate thiol to the reagent carbene at the transition states corroborates this fact.     

Molecular orbital analysis of chemical carcinogens

Simple molecular orbital calculations are employed in searching electronic parameters which may characterize the chemical carcinogens. Using frontier orbitals, the carcinogen-DNA bond formation is described as an electron transfer from the highest occupied molecular orbital (HOMO) of DNA to the lowest unoccupied molecular orbital (LUMO) of the carcinogen. Analysis of the DNA bases units shows that the electron donation occurs preferentially at the guanine site. The calculated low LUMO energy of several carcinogens indicate correctly the electrophilic character of these compounds. The difference between the carcinogen and the ultimate carcinogen is analyzed. Epoxides, free radicals, alkylating agents, and other metabolite forms are studied. A reasonable correlation is found between the LUMO energy and the carcinogenic function. © 1997 John Wiley & Sons, Inc.     

8-羟基喹啉铁配合物对锐钛矿型TiO2(101)表面的敏化机理

用密度泛函理论和DMol3程序包对锐钛矿型TiO2(101)表面复合三(8-羟基喹啉-5-羧酸)铁的敏化机理进行了研究. 计算结果表明, 该染料敏化剂经式结构的HOMO(最高占据分子轨道)-LUMO(最低未占据分子轨道)能隙非常小, 很容易受到激发; TiO2纳米晶吸附染料后, HOMO、LUMO 和费米能级都升高, 导致吸附染料后开路电压VOC升高. 并进一步探讨了三(8-羟基喹啉-5-羧酸)铁在TiO2(101)表面复合过程及作用机理.     

Electron smearing in DFT calculations: A case study of doxorubicin interaction with single‐walled carbon nanotubes

To address the choice of an appropriate value of electron smearing to facilitate self‐consistent field (SCF) convergence, we studied the interaction of doxorubicin with short armchair and zigzag single‐walled carbon nanotube models with closed caps, at the PWC/DNP level of density functional theory. By gradually reducing the electron smearing value from a large and most commonly used one of 0.005 Ha to zero (Fermi occupation), we monitored the changes in close contacts between the interacting species, total energy of the molecular system, highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energy and isosurfaces, HOMO‐LUMO gap energy, and plots of electrostatic potential. It became evident that the commonly used smearing values of ≥0.001 Ha can alter the results significantly (for example, by one order of magnitude for HOMO–LUMO gap energy). We suggest the setting of electron smearing value at 0.0001 Ha, which does not imply too high computation cost and can guarantee the results close to the ones obtained with Fermi occupation. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2011