On normalized Laplacians,multiplicative degree-Kirchhoff indices,and spanning trees of the linear [n]phenylenes and their dicyclobutadieno derivatives

Let be the molecular graph of the linear [n] phenylene with n hexagons and n − 1 squares, and let be the graph obtained by attaching four-membered rings to the terminal hexagons of . In this article, the normalized Laplacian spectrum of consisting of the eigenvalues of two symmetric tridiagonal matrices of order 3n is determined. An explicit closed-form formula of the multiplicative degree-Kirchhoff index (respectively the number of spanning trees) of is derived. Similarly, explicit closed-form formulas of the multiplicative degree-Kirchhoff index and the number of spanning trees of are obtained. It is interesting to see that the multiplicative degree-Kirchhoff index of (respectively ) is approximately to one half of its Gutman index.     

Extremal Wiener and Kirchhoff indices of globular caterpillars

The Wiener and Kirchhoff indices of a graph G are two of the most important topological indices in mathematical chemistry. A graph G is called to be a globular caterpillar if G is obtained from a complete graph K _s with vertex set {v₁,v₂,…, v _s} by attaching n _i pendent edges to each vertex v _i of K _s for some positive integers s and n₁,n₂,…,n _s, denoted by . Let be the set of globular caterpillars with n vertices (). In this article, we characterize the globular caterpillars with the minimal and maximal Wiener and Kirchhoff indices among , respectively.     

On the normalized Laplacian of Möbius phenylene chain and its applications

Let denote a molecular graph of linear [n] phenylene with n hexagons and n squares, and let the Möbius phenylene chain be the graph obtained from the by identifying the opposite lateral edges in reversed way. Utilizing the decomposition theorem of the normalized Laplacian characteristic polynomial, we study the normalized Laplacian spectrum of , which consists of the eigenvalues of two symmetric matrices ℒ _R and ℒ _Q of order 3n. By investigating the relationship between the roots and coefficients of the characteristic polynomials of the two matrices above, we obtain an explicit closed-form formula of the multiplicative degree-Kirchhoff index as well as the number of spanning trees of . Furthermore, we determine the limited value for the quotient of the multiplicative degree-Kirchhoff index and the Gutman index of .     

Study on the normalized Laplacian of a penta-graphene with applications

Let L _n denote a linear pentagonal chain with 2n pentagons. The penta-graphene (penta-C), denoted by R _n is the graph obtained from L _n by identifying the opposite lateral edges in an ordered way, whereas the pentagonal Möbius ring is the graph obtained from the L _n by identifying the opposite lateral edges in a reversed way. In this paper, through the decomposition theorem of the normalized Laplacian characteristic polynomial and the relationship between its roots and the coefficients, an explicit closed-form formula of the multiplicative degree-Kirchhoff index (resp. Kemeny's constant, the number of spanning trees) of R _n is obtained. Furthermore, it is interesting to see that the multiplicative degree-Kirchhoff index of R _n is approximately of its Gutman index. Based on our obtained results, all the corresponding results are obtained for .     

Fully numerical Hartree-Fock and density functional calculations. II. Diatomic molecules

We present the implementation of a variational finite element solver in the HelFEM program for benchmark calculations on diatomic systems. A basis set of the form is used, where (μ, ν, φ) are transformed prolate spheroidal coordinates, B _n(μ) are finite element shape functions, and are spherical harmonics. The basis set allows for an arbitrary level of accuracy in calculations on diatomic molecules, which can be performed at present with either nonrelativistic Hartree-Fock (HF) or density functional (DF) theory. Hundreds of DFs at the local spin density approximation (LDA), generalized gradient approximation (GGA), and the meta-GGA level can be used through an interface with the Libxc library; meta-GGA and hybrid DFs are not available in other fully numerical diatomic program packages. Finite electric fields are also supported in HelFEM , enabling access to electric properties. We introduce a powerful tool for adaptively choosing the basis set by using the core Hamiltonian as a proxy for its completeness. HelFEM and the novel basis set procedure are demonstrated by reproducing the restricted open-shell HF limit energies of 68 diatomic molecules from the first to the fourth period with excellent agreement with literature values, despite requiring orders of magnitude fewer parameters for the wave function. Then, the electric properties of the BH and N₂ molecules under finite field are studied, again yielding excellent agreement with previous HF limit values for energies, dipole moments, and dipole polarizabilities, again with much more compact wave functions than what were needed for the literature references. Finally, HF, LDA, GGA, and meta-GGA calculations of the atomization energy of N₂ are performed, demonstrating the superb accuracy of the present approach.     

DFT and CIS(D) theoretical study on the ground and excited states of pentanitrogen cation

Different isomers of N₅⁺ were modeled at DFT(PBE0)/aug-cc-pV(Q + d)Z, and their ground(transition) state characteristics were assessed through frequency calculations. Single-point energies were accomplished at PBE0/aug-cc-pV(5 + d)Z. Nonlinear optical susceptibilities (NLO) of isomers were accomplished using Firefly, while the linear optical invariant was examined using the finite-field method, Firefly, and modified dipole field tensor in the presence of two different screening factors. The excited states, singlets and triplets, of were modeled at the CIS and CIS(D) and then their optical parameters were estimated at TDFT(PBE0)/aug-cc-pV(Q + d)Z using Firefly. The singlet is found the most stable isomer, with the inversional rate constant larger than that of the Cs isomer and high energy barrier with the triplet counterpart. Isomers 2 , 3 , and 4 are found local minima, while 5 and 6 are saddle points: transition states between equivalent invertomers. Energy calculations of the singlet and triplet isomers were in excellent agreement with the literature. An excellent correlation is found between the average polarizability and the impulse factor. Substantial variations were found between the singlet and triplet excited states in terms of energy, geometry, and optical properties from one side and with from the other side. Reactivity indices showed that N1 and N5 are the optimum nucleophilic and electrophilic reactivity sites.     

The connective eccentricity index of graphs and its applications to octane isomers and benzenoid hydrocarbons

The connective eccentricity index (CEI) of a graph G is defined as , where ε_G(.) denotes the eccentricity of the corresponding vertex. The CEI obligates an influential ability, which is due to its estimating pharmaceutical properties. In this paper, we first characterize the extremal graphs with respect to the CEI among k-connected graphs (k-connected bipartite graphs) with a given diameter. Then, the sharp upper bound on the CEI of graphs with given connectivity and minimum degree (independence number) is determined. Finally, we calculate the CEI of two sets of molecular graphs: octane isomers and benzenoid hydrocarbons. We compare their CEI with some other distance-based topological indices through their correlations with the chemical properties. The linear model for the CEI is better than or as good as the models corresponding to the other distance-based indices.     

Is it possible to synthesize bulk salt compounds?

The existence and stability of bulk salt compounds are theoretically investigated in this study. This undertaking is carried out to address the following challenge: synthesizing a bulk salt compound containing a noble gas lighter than Kr. The reliability of theoretical calculations on systems is assessed by benchmark calculations of the well-known salt. In the benchmark calculations, a two-pronged evaluation strategy, including direct and indirect evaluation methods, is used to theoretically investigate the spectroscopic constants of cation and the existence and stability of the salt. The validity of the theoretical calculation methods in the benchmark calculations of salt allows us to adopt a similar methodology to effectively predict the existence and stability of salt compounds. Calculations based on the Born-Haber cycle using estimated lattice energies and some necessary ancillary thermochemical data show that salt compounds can be synthesized, and their upper-limit stable temperatures are estimated to be −237.589, −197.76, and −80.539°C. The salt compound is the most promising candidate. Calculations also show that the salt compounds cannot be stabilized.     

How does the pH influences the Ru-NO coordination compounds?

The pH influence has important role in the bioavailability of coordination compounds. fac-[Ru(NO)Cl₂(κ³N⁴,N⁸,N¹¹[1-carboxypropyl]cyclam)]⁺, 1 , and the species found at different pHs, 2 - 4 , were investigated. One series of computational methodologies has been used to investigate these compounds. One special highlight is to interacting quantum atoms method, where the total interaction energy, , between two atoms has been used as base to estimate the chemical bonds strength. The deprotonation of -CO₂H, 1 ➔ 2 (pK_a = 3.3), creates a hydrogen bond in the complex 2 , N( 3 )-H⋯ ·OCO⁻, with a more favorable than the presents in 1 , N( 3 )-H⋯ ·OCOH. There are no changes in in Ru-NO bond. The second deprotonation occurs in the N(2) atom of the cyclam group, 2 ➔ 3 (pK_a = 8.0). It promotes an increase in the covalent character of Ru-N( 2 ). In contrast, there is no changes in Ru-N( 5 )O bond. For higher pHs, there is a 3 ➔ 4 equilibrium (pK_a = 11.5) and the conversion of Ru-N( 5 )O for Ru-N( 5 )O₂. The Ru-N( 5 ) of 4 shows a larger ionic character than 3 . Thus, Ru-NO in 1 - 4 has worthy stability about a large pH range, showing potential application as NO scavengers.     

Mind the correct basis set: A case study for predicting gas phase acidities of small compounds using calculations from first principles

Some of the most popular computational methods have been utilized to determine a dependency of the acidity trend of the first‐row hydrides on a choice of basis set. For about three decades, methyl anion ( ) was known as the strongest base but after Tian et al. were able to produce the gas phase lithium monoxide anion (LiO–) they discovered it was a stronger base than (Tian et al., Proc Natl Acad Soc USA 2008, 105, 7647). Furthermore, the authors confirmed their experimental results using high‐level ab initio methods, namely W1 and W2C composite methods, as well as complete active space‐averaged quadratic coupled cluster and Brueckner Doubles with triple excitation contribution (BD(T)) within the aug‐cc‐pVQZ basis set. These methods are highly demanding in terms of the computational effort as well as a level of expertise needed from the user to correctly conduct such calculations. We have shown that the proper acidity trend, that is, , can be obtained with less expensive, ”black‐box” type methods if only the basis set is properly chosen. Our results prove that the diffuse augmented basis sets are absolutely necessary for appropriate predictions of acidities. Our calculations show that the correct order of is achieved by augmenting relatively small cc‐pVXZ (X = D,T) basis sets. A similar effect is observed for the family of Pople's basis sets. Our estimate for with CCSD(T)/aug‐cc‐pVTZ was 423.8 kcal/mol, which agrees very well with the experimental value 425.7 ± 6.1 kcal/mol. An important finding is that the proper acidity trend may be reversed if the basis sets are not correctly selected. © 2014 Wiley Periodicals, Inc.     

Explicitly correlated variational estimates of the energy levels of negative hydrogen ion under spatial confinement

Comprehensive investigations on the structural modifications of negative hydrogen ion within an impenetrable spherical domain has been performed in the framework of Ritz variational method. Electron correlation plays a major role in the formation of H^– ion. The Hylleraas‐type basis set expansion of wave function considered here incorporates the effect of electron correlation in an explicit manner. Energy values of and 1sn states of H^– ion within confined domain have been calculated. Although the singly excited states do not exist for a “free” H^– ion, well converged energy values of such states have been found within a wide range of confinement radius. The thermodynamic pressure felt by the ion inside the sphere is also estimated. The general trend shows successive destabilization of the excited energy levels with increase of pressure. The contribution of angular correlation in the energy values have been estimated. Evolution of and energy levels of H^– ion as quasi‐bound states are being reported.     

Simulated annealing‐based optimal control over tunneling process through SDWP and Eckart barrier: A momentum basis representation

For a reaction to proceed via tunneling mechanism, it is essential that the reactants will cross the potential barrier (E_P), where its initial energy (E₀) is below the potential barrier E_P. Tunneling probability τ is defined as the probability of having momentum higher than k_m, where . In the momentum basis representation, τ can be directly calculated by integrating from the limit k_m to infinity, where is the wave function in the momentum space. Instead of the continuous basis, if we chose momentum grid space, τ can be expressed as . Our target here is to increase this τ by applying a polychromatic field, so that the reaction rate can be enhanced. By applying Simulated Annealing technique we have designed some polychromatic electric fields, spatially symmetric and asymmetric type, which enhances the tunneling rate in symmetric double well system and Eckart barrier confined in an infinite well.     

Exponentially correlated Hylleraas-configuration interaction studies of atomic systems. II. Non-relativistic energies of the 1 through 6 states of the Li+ ion

The exponentially correlated Hylleraas-configuration interaction wave function (E-Hy-CI) is a generalization of the Hylleraas-configuration interaction (Hy-CI) in which the single of an Hy-CI wave function is generalized to the generic type . This type of correlation has the right behavior both in the vicinity of the cusp and as goes to infinity; this work shows that wave functions containing both linear and exponential factors converge more rapidly than either one alone for low-lying excited states of ¹S symmetry. E-Hy-CI variational calculations with up to 8568 configurations lead to a nonrelativistic energy of ?7.2799 1341 2669 3059 6491 6759 hartree for the 1 ¹S ground state of the Li+ ion.     

Theoretical investigation of geometry and stability of small lithium‐iodide LinI (n = 2–6) clusters

We present theoretical investigation of the structural characteristics and stabilities of neutral and positively charged Li_nI (n = 2‐6) species. The structural isomers were found by using a randomized algorithm to search for minima structures, followed by B3LYP optimizations; the single‐point RCCSD(T)/cc‐pwCVTZ(‐PP) calculations were performed in order to compute relative energies, binding energies per atom, adiabatic and vertical ionization energies, and dissociation energies. Stability was compared to the pure lithium clusters; there is a typical odd‐even alternation; iodine doped clusters are more stable than pure lithium clusters. Lithium “cage” transfers its valence electron to the iodine atom to form neutral and cationic clusters. An electron departures the lithium cage upon ionization. An important reason for the larger stability of closed‐shell species is the existence of the HOMO 3c/2e natural bond orbitals. © 2013 Wiley Periodicals, Inc.     

Comparison of triel bonds with different chalcogen electron donors: Its dependence on triel donor and methyl substitution

The complexes between R₃Tr (Tr = B, Al, and Ga; R = H, F, Cl, and Br) and H₂X (X = O, S, and Se) were theoretically studied. The interaction energies of R₃Al⋯H₂X and R₃Ga⋯H₂X are consistent with the electronegativity of the halogen atom R (R ≠ H), but an opposite dependence is found for R₃B⋯H₂X. The triel bond of R₃Tr⋯H₂X is weaker for the heavier chalcogen donor. The dependence of triel bonding strength on the triel atom is complicated, depending on the nature of R and X. The methyl substitution of H₂X causes a substantial increase in the interaction energy from −5.74 kcal/mol to −22.88 kcal/mol, and its effect is relevant to the nature of Tr, X, and R groups. For the S and Se donors, the increased percentage of interaction energy is almost the same due to the methyl substitution, which is larger than that of the O analogue. In most triel-bonded complexes, electrostatic dominates and polarization has comparable contribution. However, polarization plays a dominant role in R₃B⋯ and R₃B⋯ (R = Cl and Br; R′ = H and Me).     

Improved description of the orbital relaxation effect by practical use of the self‐energy

The self‐energy shift in the orbital relaxation (OR) term of the polarization propagator complete through the second‐order is presented. In combination with the optimal damping parameter in the OR term, the modified propagator produces the excitation energy of the coupled‐cluster with singles and doubles (CCSD) accuracy. The self‐energy shift requires the floating‐point operation of , where N refers to the magnitude of the molecular size. Because the second‐order polarization propagator requires the floating‐point operation of , the additional computational effort to construct the self‐energy is negligibly small. Numerical results are shown for several molecules including glycine, 2,3,5,6‐tetrafluorobenzene, and naphthalene, and promising agreements with those of CCSD are confirmed within less than 0.2 eV. The basis set dependence is also tested for the water molecule using aug‐cc‐pV NZ (N = D–7), where this newly developed approach mimics the behavior of the CCSD values. The self‐energy shifting for the second‐order response matrix in combination with the use of a dumping parameter is efficiently implemented for calculations of medium‐sized molecular systems, including glycine and naphthalene. The developed approach provides CCSD‐like accuracy at a more affordable computational expense. © 2014 Wiley Periodicals, Inc.     

Dynamical Jahn-Teller effect in the first excited

Jahn-Teller effect of C₆₀ monoanion in the first electronically excited states was theoretically investigated. The orbital vibronic coupling parameters for t_1g next lowest unoccupied molecular orbitals were derived from the Kohn-Sham orbital levels calculated using a frozen phonon approach with both hybrid B3LYP and CAM-B3LYP functionals, which take long-range interaction correction into consideration. With these coupling parameters, the vibronic states of first excited were derived by exactly diagonalizing dynamical Jahn-Teller Hamiltonian. The results showed that dynamical Jahn-Teller effects are more significant in the first excited than those in the ground electronic states. This work also clarified that CAM-B3LYP gives results closer to experimental data than B3LYP.     

Virial relations in density embedding

The accuracy of charge-transfer excitation energies, solvatochromic shifts, and other environmental effects calculated via various density-embedding techniques depend critically on the approximations employed for the nonadditive noninteracting kinetic energy functional, . Approximating this functional remains an important challenge in electronic-structure theory. To assist in the development and testing of approximations for , we derive two virial relations for fragments in molecules. These establish separate connections between the nonadditive kinetic energies of the noninteracting and interacting systems of electrons, and quantities such as the electron-nuclear attraction forces, the partition (or embedding) energy and potential, and the Kohn-Sham potentials of the system and its parts. We numerically verify both relations on diatomic molecules.     

3D‐QSAR studies and molecular design on a novel series of pyrimidine benzimidazoles as Lck inhibitors

The development of selective lymphocyte‐specific kinase (Lck) inhibitors has attracted much attention for the research of the treatment of T‐cell mediated autoimmune and inflammatory diseases. In the present work, three‐dimensional quantitative structure–activity relationship (3D‐QSAR) analyses are performed on a novel series of 4‐amino‐6‐benzimidazole‐pyrimidines acting as Lck inhibitors. The established 3D‐QSAR models show significant statistical quality and satisfactory predictive ability, with high q² and R² values: the comparative molecular field analysis (CoMFA) model (q² = 0.802, R² = 0.991), and the comparative molecular similarity indexes analysis (CoMSIA) model (q² = 0.731, R² = 0.982). The systemic external validation indicates that both CoMFA and CoMSIA models are quite robust and possess high predictive abilities with values of 0.881 and 0.877, values of 0.897 and 0.847, values of 0.897 and 0.850, and values of 0.897 and 0.854, respectively. Several key structural features accounting for the inhibitory activities of these compounds are discussed. Based on established models and design considerations, six new compounds with significantly improved activities are theoretically designed, which still await experimental confirmation and evaluation. These theoretical results may provide a useful reference for understanding the action mechanism and designing novel potential Lck inhibitors. © 2014 Wiley Periodicals, Inc.     

Unexpected properties of non‐autoionizing doubly excited states of the H2 molecule

We present accurate calculations of the non‐autoionizing and doubly excited states of the H₂ molecule using full configuration interaction with Hartree–Fock molecular orbitals and Heitler–London atomic orbitals. We consider the united atom configurations from He(2p2p) up to He(2p8g) and dissociation products from H₂(2p + 2p) up to H₂(2p + 6?). Born–Oppenheimer calculations are carried out with extended and optimized Slater‐type orbitals for a total of 40 states, 10 for each symmetry, covering the internuclear distances from the united atom to dissociation, which, for some states, is reached beyond 100 a₀. Occurrences of repulsive states cleanly interlaced between bound states with many vibrational levels are reported. Some of the potential minima are deep enough to accommodate many vibrational levels (up to 50). Noteworthy large equilibrium minima, like R_eq = 46.0 a₀ in the state dissociating as (2p + 6h) and with 18 vibrational levels. The occurrence of vertical excitations from the singly excited manifolds is analyzed. Several states present double minima generated by avoided crossings, some with a strong ionic character. © 2016 Wiley Periodicals, Inc.