Effects of nucleobase metalation on frontier molecular orbitals: potential implications for pi-stacking interactions with tryptophan

Biochemical recognition processes mediated through pi-stacking interactions are a potential target for rational drug synthesis. A combination of electrostatic, hydrophobic, solvation, charge-transfer, induction, and dispersion interactions has been used to account for the three-dimensional arrangements observed in such motifs. A principal example involves the interaction of purine and pyrimidine rings of nucleic acids with aromatic amino-acid residues such as tryptophan, phenylalanine, and tyrosine. Protonation, alkylation, or coordination of a metal ion such as Pd(II) or Pt(II) to a nucleobase strengthens this interaction by lowering the energy of the lowest unoccupied molecular orbital (LUMO) of the modified nucleobase and improving overlap with the highest occupied molecular orbital (HOMO) in N-acetyl tryptophan. The relative energy difference between the frontier orbitals of isolated molecules, obtained using Density Functional Theory (DFT), is explored as a predictive tool for the strength of the pi-stacking interaction of the nucleobase/tryptophan pair. From the optimized structures of these species, evaluation of the donor-acceptor HOMO-LUMO gap (Deltaepsilon d-->a) suggests that this parameter is a promising predictor of pi-stacking strength for the donor-acceptor pairs presented in this study. The analysis correlates well with experimental association constants, measured by fluorescence spectroscopy, of metallated and alkylated nucleobases with tryptophan in comparison to free nucleobases.     

Trap mechanism based on frontier molecular orbitals of additives in polyethylene insulators: A theoretical study and molecular design strategy

In this work, the energy gaps (E_g) of highest occupied orbitals and lowest unoccupied orbitals, trap energies (E_t(e) and E_t(h)) and excited energies of polyethylene model compound, typical defect compound, acetophonene, and 33 designed additives are obtained using density functional method at B3LYP/6–311+G(d, p) level. The correlation between trapping‐electrons (holes) abilities of additives and molecular frontier orbitals is established, and a new understanding for trap mechanism based on chemical molecular orbital levels is given for the first time which could be used to filter qualitative additives as voltage stabilizers of polyethylene. The role of trap energies and the energy gaps on discussing space charge accumulation and electric breakdown is analyzed in detail. A molecular design strategy for potential additives of cross‐linked polyethylene insulated high‐voltage cable is shown based on conjugation effect, substituents character, and polycyclic aromatic compounds. © 2015 Wiley Periodicals, Inc.     

Simplified box orbitals: A spatially restricted alternative to the slater‐type orbitals

We introduce a new type of spatially restricted basis function (zero beyond a characteristic r₀ value of the radial coordinate) that makes it possible to obtain, in nonconfined systems, similar results to STO functions. This is important because the use of this kind of functions enables the exact application a sort of zero differential overlap approximation to calculate properties of large systems. Our functions are a modification of the BO‐xZ box orbitals introduced by Lepetit et al. First, we replaced these orbitals by a function that is easier to obtain and generalize, that we named “simplified box orbital” (SBO), and we have shown some advantages of the SBO over BO and standard STO functions. Second, we obtained Gaussian developments for both the original BO orbitals and the new SBO orbitals. In this way, it becomes possible to manage our SBO orbitals with standard quantum chemistry software like GAUSSIAN or similar programs. © 2014 Wiley Periodicals, Inc.     

Liquid crystal Pancharatnam-Berry phase lens with spatially separated focuses

In this paper, we proposed and fabricated a liquid crystal (LC) lens with spatially separated focuses via liquid crystal photoalignment technology. The novel lens is an integration of the polarisation grating and conventional LC lens. The two focuses of that new lens, one of which is real while the other is virtual, can be spatially separated. When combined with normal convex lens and illuminated by a linearly polarised beam, the two emergent light beams become all convergent and the two focuses are separated in three-dimension space. Moreover, the focal lengths of the lens system can be artificially controlled by adjusting the distance between our new lens and the conventional lens. Our results achieve the potential of LC lens’ application in imaging devices such as multifocal cameras, bifocal eyeglasses and so on.     

Reference program for molecular calculations with Slater-type orbitals

A program for computing all the integrals appearing in molecular calculation with Slater-type orbitals is reported. The program is mainly intended as a reference for testing and comparing other algorithms and techniques. An analysis of the performance of the program is presented, paying special attention to the computational cost and the accuracy of the results. Results are also compared with others obtained with Gaussian basis sets of similar quality. © 1998 John Wiley & Sons, Inc. J Comput Chem 19: 1284–1293, 1998     

Preferential site of attack on fullerene cations: frontier orbitals and rate coefficients

An analysis of reaction efficiency is presented for reactions of carbonaceous ions and molecules. Our results show that the combination of experimental rate-coefficient measurements and computations of the condensed Fukui functions of frontier molecular orbitals and pyramidal angles of pi orbitals is very useful for elucidating the reactive sites on fullerene carbon clusters in the gas phase.     

Extremely localized molecular orbitals: theory and applications

Orbitals that are extremely localized on molecular fragments represent a powerful tool for a number of purposes: to cite a few examples, they allow to reduce strongly the complexity of calculations on large systems and are easily transferable from one molecule to another, providing a suitable and efficient way to build up the electronic structure of large molecules. Recently, we have developed efficient algorithms to determine extremely localized molecular orbitals (ELMOs), which will be reviewed in this paper. As a rigorous localization is strictly connected to a reduction in the number of variational parameters, which reflects into an increased value of the associated energy with respect to the Hartree Fock value, we have developed a number of strategies to relax the wavefunction built up using transferred localized orbitals. The extreme localization has also been exploited in connection with the “Divide and Conquer” technique to determine the electron densities of large polypeptides assembled from orbitals computed on small model molecules. Moreover, we will discuss the recent application of the ELMOs in the framework of the hybrid QM/MM methods to describe the frontier region. We will also show that the ELMOs can be used to extract chemical interpretations from numerical results. A variety of applications will be presented.     

Correlation of the molecular orbitals of organic sulfides (selenides) and five-membered heterocyclic compounds by photoelectron spectroscopy

The structure and the correlation of the molecular orbitals were studied for divinyl chalcogenides and the isoelectronic five-membered heterocyclic compounds by photoelectron spectroscopy (PES). It was shown that the two frontier orbitals are inverted in the transition from divinyl sulfide to thiophene, while the heterocyclization of divinyl selenide is accompanied by quasidegeneration. According to PES, the orbital structure of the alkyl vinyl chalcogenides does not depend on the nature of the heteroatom (S, Se) or on the structure of the alkyl radical: ₂ < ₁ < ₂ < ₂. Linear correlations were obtained between the energies of the ₁ and ₂ MOs of the investigated groups of compounds, i.e., one for the vinyl Sulfides (selenides) and thiophenes (selenophenes) and another for the saturated derivatives of sulfur and selenium. The correlations in the compounds of the various chalcogens do not coincide, although they are similar.Translated from Izvestiya Akademii Nauk SSSR, Seriya Khimicheskaya, No. 10, pp. 2317–2324, October, 1991.     

Hydroxydialkylamino cruciforms: amphoteric materials with unique photophysical properties

Two amphoteric cruciforms 6 and 7 (XF; 4,4'-[(1E,1'E)-(2,5-bis{[4-(dibutylamino)phenyl]ethynyl}-1,4-phenylene)bis(ethene-2,1-diyl)]diphenol, 4,4'-[{2,5-bis[(E)-4-(dibutylamino)styryl]-1,4-phenylene}bis(ethyne-2,1-diyl)]diphenol) were prepared by a Horner reaction followed by a Sonogashira coupling and subsequent deprotection. The XFs display significant changes in absorption and emission when exposed to trifluoroacetic acid, tetrabutylammonium hydroxide, and metal triflates. The substitution pattern of 6 and 7 leads to spatial separation of the frontier molecular orbitals, which allows the HOMO or LUMO of the XF to be addressed independently by acidic or basic agents. XF 6, which has hydroxyl groups on the styryl axis, displays changes in emission color upon exposure to ten amines in eight different solvents. The change in fluorescence upon the addition of amines was analyzed by linear discriminant analysis. These XFs may have potential in sensor applications for metal cations and amines.     

Optimal virtual orbitals to relax wave functions built up with transferred extremely localized molecular orbitals

Extremely localized molecular orbitals (ELMOs), namely orbitals strictly localized on molecular fragments, are easily transferable from one molecule to another one. Hence, they provide a natural way to set up the electronic structure of large molecules using a data base of orbitals obtained from model molecules. However, this procedure obviously increases the energy with respect to a traditional MO calculation. To gain accuracy, it is important to introduce a partial electron delocalization. This can be carried out by defining proper optimal virtual orbitals that supply an efficient set for nonorthogonal configurations to be employed in VB-like expansions.     

Density functional theory (DFT) investigation of molecular structure and frontier molecular orbitals (FMOs) of P-N,N-dimethylaminobenzylidenemalononitrile (DBM)

P-N,N-dimethylaminobenzylidenemalononitrile (DBM) dye belongs to a class of organic compounds known as molecular rotors. Its optimized geometry and frontier molecular orbitals (FMOs), before and after ultraviolet (UV) irradiation, were obtained by DFT/B3LYP level with complete relaxation in the potential energy surface using 6-311++G(d,p) basis set. It is found that the length of C-C bonds of the DBM molecule increases after the UV irradiation, which leads to an increase in its dipole moment making it as a promising material for solar cell applications. Also, its HOMO-LUMO gap decreased from 3.46 to 3.34 eV. From the cyclic voltammetry measurements the value of HOMO-LUMO gap is equal to 3.21 eV. This means that B3LYP/6-311++G(d,p) level of theory is the best one for calculations.     

The scaling approach to multicenter molecular integrals with Slater-type orbitals

A scaling approach to multicenter molecular integrals with Slater-type orbitals (STOs) is presented. The result is significant in that it shows (1) the existence of a simple relationship between multicenter integrals and (2) an implied computational savings. Operation count estimates indicate that the significant savings would occur for a system having large numbers of STOs on each atom.     

Synthesis of p-tert-butylthiacalix[4]arene with spatially separated phosphoryl and amino groups

Russian Journal of General Chemistry - The reactions of p-tert-butylthiacalix[4]arenes containing phthalimide fragments with diethyl-[(p-toluenesulfonyl)oxymethyl)]phosphonate were used to...     

Calculating overlap intergals with slater-type orbitals in the molecular coordinate system

Kirov Azerbaidzhan University. Translated from Zhurnal Strukturnoi Khimii, Vol. 28, No. 5, pp. 148–149, September–October, 1987.     

Calculation of localised molecular orbitals with the Foster—Boys criterion

The methods suggested by Barr and Basch to improve the convergence behaviour of localization methods are tested within the framework of the Foster—Boys criterion.     

New program for molecular calculations with Slater‐type orbitals

A new program for computing all the integrals appearing in molecular calculations with Slater‐type orbitals (STO) is reported. This program follows the same philosophy as the reference pogram previously reported but introduces two main changes: Local symmetry is profited to compute all the two‐electron integrals from a minimal set of seed integrals, and a new algorithm recently developed is used for computing the seed integrals. The new code reduces between one and two orders of magnitude the computational cost in most polyatomic systems. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 148–153, 2001     

Design of donors with broad absorption regions and suitable frontier molecular orbitals to match typical acceptors via substitution on oligo(thienylenevinylene) toward solar cells

A series of oligo(thienylenevinylene) derivatives with or without thieno[3,2‐b]thiophene analogs as cores and three types substituent has been investigated at the PBE0/6‐31G(d) and the TD‐PBE0/6‐31+G(d,p) levels to design materials with high performance such as suitable frontier molecular orbital (FMO) energies to match those of [6,6]‐phenyl‐C₆₁‐butyric acid methyl ester (PCBM) and its derivatives, broad absorption spectra, higher and balance transfer property, and better stability. The results reveal that fused cores have slight effects on photophysical properties of investigated derivatives. The electron‐withdrawing or push–pull substituents result in red shifts of absorption spectra and better stabilities for investigated derivatives. The calculated reorganization energies of designed derivatives suggest them to be good potential ambipolar transport materials under the proper operating conditions. The promising donors for PCBM, bisPCBM, PC70BM, and indene‐C₆₀ bisadduct (ICBA) as acceptors are recommended theoretically for solar cells based on the proper match for FMOs between donors and acceptors. Moreover, we have also predicted the mobility of designed molecule with better performance. © 2012 Wiley Periodicals, Inc.     

Communication: Superatom molecular orbitals: new types of long-lived electronic states

We present ab initio calculations of the quasiparticle decay times in a Buckminsterfullerene based on the many-body perturbation theory. A particularly lucid representation arises when the broadening of the quasiparticle states is plotted in the angular momentum (l) and energy (ε) coordinates. In this representation the main spectroscopic features of the fullerene consist of two occupied nearly parabolic bands, and delocalized plane-wave-like unoccupied states with a few long-lived electronic states (the superatom molecular orbitals, SAMOs) embedded in the continuum of Fermi-liquid states. SAMOs have been recently uncovered experimentally by Feng et al. [Science 320, 359 (2008)] using scanning tunneling spectroscopy. The present calculations offer an explanation of their unusual stability and unveil their long-lived nature making them good candidates for applications in the molecular electronics. From the fundamental point of view these states illustrate a concept of the Fock-space localization [B. L. Altshuler, Y. Gefen, A. Kamenev, and L. S. Levitov, Phys. Rev. Lett. 78, 2803 (1997)] with properties drastically different from the Fermi-liquid excitations.     

Continuous symmetry measures of irreducible representations: application to molecular orbitals

The formalism of continuous symmetry measures is extended to describe the extent to which a function, such as a molecular orbital, transforms under the symmetry operations of a given point group according to each irreducible representation of this group. For distorted molecules we are able to calculate the degree to which any molecular orbital transforms with respect to the irreducible representations of the pseudosymmetry group that is valid for a higher symmetry, idealized geometry, showing which irreducible representations participate in each molecular orbital upon symmetry loss in the geometry of the nuclear framework.