Large Interaction Energy Research Articles

Conformational, spectroscopic and nonlinear optical properties of biologically active N,N-dimethyltryptamine molecule: A theoretical study

The effective psychoactive properties of N,N-dimethyltryptamine (DMT) known as the near-death molecule have encouraged the imagination of many research disciplines for several decades. Although there is no theoretical study, a number of paper composed by experimental techniques have been reported for DMT molecule. In this study, the molecular modeling of DMT was carried out using B3LYP and HSEh1PBE levels of density functional theory (DFT). Our calculations showed that the energy gap between HOMO and LUMO is low, demonstrating that DMT is a biologically active molecule. Large hyperconjugation interaction energies imply that molecular charge transfer occurs in DMT. Moreover, NLO analysis indicates that DMT can be used an effective NLO material.

Theoretical studies on interaction of anticancer drugs (dacarbazine, procarbazine and triethylenemelamine) with normal (AT and GC) and mismatch (GG, CC, AA and TT) base pairs

This study is an attempt to gain a better understanding of the physicochemical interaction between novel anticancer drugs and DNA bases. We have employed quantum chemical tools to explore the interaction of a few anticancer drugs [namely procarbazine (PR), dacarbazine (DC) and triethylenemelamine (TR)] with isolated normal (GC and AT) and mismatch (AA, CC, GG and TT) base pairs. The molecular geometries, electronic structural stability, vibrational energies, chemical reactivity and other electronic properties were studied using MP2/6-311+G**, B3LYP/6-311+G** and M05-2X/6-311+G** methods. The optimised geometries of the usual and mismatch base pairs are almost planar whereas the geometries of drug-interacting complexes deviate from planarity. The presence of steric hindrance and π-bond overlaps between C–C bonds in the complexes has distorted the planarity of the four- and five-member rings in the base pairs. Among the three drugs chosen, DC and PR bond well with normal and mismatch base pairs with large interaction energy. The electron density (ED) difference maps of the most stable GG–DC, GG–PR and GG–TR drug-interacting complexes show the information about sharing of ED and gain or loss of ED within the interacting molecules. The stabilisation energy of the charge transfer interaction between the relevant donor–acceptor orbital of GG–DC and GC–DC complexes has been found to be around 16 kcal/mol and GG–PR and GC–PR complexes has been found to be around 12 kcal/mol. But, for the GG–TR and GC–TR complexes, the stabilisation energy is found to be less than 6 kcal/mol. Moreover, the topological analysis of hydrogen bond network of DC and PR drug-interacting complexes have high electron and Laplacian density with structural stability at the bond critical points (BCPs), while compared TR drug-interacting complexes by atoms in molecules and natural bond orbital analysis. Finally, we may conclude that the drugs DC and PR are highly efficient drugs to target normal and mismatch base pair for control and inhibition of DNA replication.

Single Electron Pnicogen Bonded Complexes

A theoretical study of the complexes formed by monosubstituted phosphines (XH2P) and the methyl radical (CH3) has been carried out by means of MP2 and CCSD(T) computational methods. Two minima configurations have been obtained for each XH2P:CH3 complex. The first one shows small P-C distances and, in general, large interaction energies. It is the most stable one except in the case of the H3P:CH3 complex. The second minimum where the P-C distance is large and resembles a typical weak pnicogen bond interaction shows interaction energies between -9.8 and -3.7 kJ mol(-1). A charge transfer from the unpaired electron of the methyl radical to the P-X σ* orbital is responsible for the interaction in the second minima complexes. The transition state (TS) structures that connect the two minima for each XH2P:CH3 complex have been localized and characterized.

Electronic and bonding properties of mono-ruthenium-substituted Keggin-type polyoxometalates: a theoretical study of [{PW11O39}RuII/III(L)] n − (L = dimethyl sulfoxide (DMSO), water, pyridine, and ammonia) and [{GeW11O39}RuII(DMSO)3(H2O)]6−

The electronic structure and bonding feature of a series of mono-ruthenium-substituted Keggin-type polyoxometalates (POMs) have been investigated by using density functional theory (DFT) calculation, natural bond orbital (NBO) analysis and energy-decomposition analysis (EDA). A comparison of the electronic properties of two known dimethyl sulfoxide (DMSO)-supported mono-ruthenium-substituted Keggin-type POMs shows that both complexes have the analogous frontier-molecular orbital feature. One of them possesses a relatively small HOMO–LUMO gap because of the high HOMO energy level. This difference comes from a high composition of POM ligand with antibonding feature in HOMO. In addition, three typical Keggin-type POM complexes [{PW11O39}RuII/III(L)]n− (L = H2O, C5H5N, NH3) have also been explored according to our computational studies. The NBO analysis shows that the RuII/III–L bond comes from donor–acceptor interactions between the end ligand and the ruthenium (II/III) centre. The EDA shows that the POM complex [{PW11O39}RuII(C5H5N)]5− has much stronger RuII–L bond than ammonia-supported Keggin-type POM [{PW11O39}RuII(NH3)]5−. And the enhancement of the RuII–L bonding interaction in [{PW11O39}RuII(C5H5N)]5− is mainly due to the large orbital interaction energy ΔEorb. The ammonia-supported Keggin-type POM [{PW11O39}RuII(NH3)]5− and the aqua-ruthenium derivative [{PW11O39}RuII(H2O)]5− have an analogous magnitude of the total bond energy. This result supports a non-aqueous environment for synthesis of an ammonia-supported Keggin-type POM [{PW11O39}RuII(NH3)]5−.

Coupled cluster and density functional investigation of the hydrogen bond between halides, paraffines, olefins, and alkynes

By means of coupled cluster and density functional M06-2X calculations we have studied the directionality and energetics of the hydrogen bond (HB) between halides and the following H donors: methane, ethylene, and acetylene. The largest interaction energy was obtained for acetylene, the molecule in which the hydrogen atoms present the largest positive charge. For the complex (X��� HCCH) - , fluoride presented a different behavior since acetylene donates a hydrogen to fluoride and the (HF��� CCH) - complex was formed. We found that for ethylene there is a strong competition between the mono- dentate- and bidentate-like structures. Because of its small size, fluoride leads to a monodentate complex with C2H4. However, as we move down in the periodic table, the bidentate-like structure becomes more stable. In effect, for chloride and bromide they are nearly isoenergetic, while for iodide the bidentate-like complex is formed. These present results question previous investigations about the directionality of the HB in halide-ethylene complexes.

Theoretical investigation on the 2e/12c bond and second hyperpolarizability of azaphenalenyl radical dimers: Strength and effect of dimerization

An increasing number of chemists have focused on the investigations of two-electron/multicenter bond (2e/mc) that was first introduced to describe the structure of radical dimers. In this work, the dimerization of two isoelectronic radicals, triazaphenalenyl (TAP) and hexaazaphenalenyl (HAP) has been investigated in theory. Results show TAP2 is a stable dimer with stronger 2e/12c bond and larger interaction energy, while HAP2 is a less stable dimer with larger diradical character. Interestingly, the ultraviolet-visible absorption spectra suggest that the dimerization induces a longer wavelength absorption in visible area, which is dependent on the strength of dimerization. Significantly, the amplitude of second hyperpolarizability (γ(yyyy)) of HAP2 is 1.36 × 10(6) a.u. that is larger than 7.79 × 10(4) a.u. of TAP2 because of the larger diradical character of HAP2. Therefore, the results indicate that the strength of radical dimerization can be effectively detected by comparing the magnitude of third order non-linear optical response, which is beneficial for further theoretical and experimental studies on the properties of complexes formed by radical dimerization.

Density functional theory calculations of hydrogen adsorption on Ti-, Zn-, Zr-, Al-, and N-doped and intrinsic graphene sheets

The effect of different doped atoms on the interactions between graphene sheets and hydrogen molecules were investigated by density functional theory calculations. The interactions between graphene sheets and hydrogen molecules can be adjusted by doped atoms. The Ti-doped graphene sheet had the largest interaction energy with the hydrogen molecule (approximately −0.299 eV), followed by the Zn-doped graphene sheet (about −0.294 eV) and then the Al-doped graphene sheet (approximately −0.13 eV). The doped N atom did not improve the interactions between the N-doped graphene sheet and the hydrogen molecule. Our results may serve as a basis for the development of hydrogen storage materials.

Decafluorocyclohex-1-ene at 4.2 K – crystal structure and theoretical analysis of weak interactions

The crystal structure of 1,2,3,3,4,4,5,5,6,6-decafluorocyclohex-1-ene (decafluorocyclohex-1-ene, C6F10) was solved in direct space from neutron powder diffraction data previously collected at 4.2 K [Pawley, G. S. (1981). J. Appl. Cryst. 14, 357-361] and refined by energy minimization in the solid state. To optimize the positions of the 64 atoms in the monoclinic computational cell the PBESOL and hybrid PBE0 functionals were used. The crystal structure of the title compound, which is liquid at room temperature, is built of antiparallel pairs of molecules assembled into molecular columns stacked along the a axis. Dominating the crystal-building forces are weak intermolecular dispersion interactions. Bonding conditions in the structure were analysed by theoretical molecular calculations of representative next-neighbor molecular dimers carried out using dispersion-corrected density functional theory (DFT) functionals and the SCS-MP2 wavefunction method. The largest interaction energy is of the order of ∼ 21 kJ mol(-1), above the interaction energy of a benzene dimer (11.3 kJ mol(-1)) and close to that of a water dimer (20.9 kJ mol(-1)). The interaction energy for the second most stable dimer can be compared with either that of a benzene dimer or of a C-H...π hydrogen bond. The remaining five weakly interacting dimers (∼ 4.2-8.4 kJ mol(-1)) can be characterized as having stronger interactions than those of methane dimers (-2.2 kJ mol(-1)), but weaker than those of benzene molecule pairs or weak C-H...C interactions for instance.

A Tunable Coupler with ScS Quantum Point Contact to Mediate Strong Interaction Between Flux Qubits

In this paper we propose a kind of quantum inductance couplers (QUINC) which represents a superconducting loop closed by ScS quantum point contact, operating in deep quantum low-temperature regime to provide tunable (Ising-type) ZZ interaction between flux qubits. This coupler is shown to be well tunable by an external control magnetic flux and to provide large inter-qubit interaction energies $|J/k_{\rm B}|\simeq1$ K thus being very promising as a qubit-coupling device in a quantum register as well as for studying fundamental low-temperature quantum phenomena. Some entanglement measures of a two-qubit system are analyzed as functions of inter-qubit interaction strength.

Hydrocarbon Chain Length Induces Surface Structure Transitions in Alkanethiolate–Gold Adatom Self-Assembled Monolayers on Au(111)

A detailed density functional calculation (DFT) study including van der Waals (vdW) dispersion forces of different adatom-containing models (RS–Auad–SR) at saturation coverage for methanethiol (MT), butanethiol (BT), and hexanethiol (HT) on Au(111) is presented. The stability analysis of these lattices shows a transition from the (3 × 4) to the c(4 × 2) surface structure when the number of C atoms in the alkanethiol chain is larger than 2, fairly predicting recent experimental observations for these systems. The transition takes place when the smaller energy needed to reconstruct the Au(111) surface and the larger binding energy for MT in the (3 × 4) MT lattice is compensated by a larger interaction energy between hydrocarbon chains in the c(4 × 2) lattice for BT and HT. Our calculations therefore explain why the (3 × 4) lattice is more stable for MT and ethanethiol (ET) while the c(4 × 2) lattice predominates for longer alkanethiols, thus shedding light on the behavior of alkanethiol self-assembled monol...

The insertion of gas molecules into polyhedral oligomeric silsesquioxane (POSS) cages: understanding the energy of insertion using quantum chemical calculations

Density functional theory (DFT) calculations using the B3LYP and ωB97XD functionals and Møller-Plesset (MP2) calculations have been used to determine the energy of insertion of seven molecules (CO2, N2, O2, CO, CH4, He and H2O) into two sizes of polyhedral oligomeric silsesquioxane (POSS) cages, T10 and T12. Geometry optimization results of each molecule inserted into the center of the POSS cage and transition-energy searches of the molecules in the largest face of both T10 and T12 (identified as the Si5 face) are discussed. The main factors that affect the energy of a molecule in a particular POSS cage are the size (number of atoms) and shape of the POSS cage and the strength of dispersion and electrostatic interactions. The largest of the molecules, CO2 and CH4, have the largest interaction energies within the center and the face of the T10 and T12 cages. Interaction energies for the diatomic molecules increase in the order H2 < O2 < N2 ∼ CO and differences between interaction energies can be attributed, in part, to differences in electron transfer between the cage and molecule. Electrostatic interactions also play a significant role in determining the interaction energy. For example, H2 and He are only slightly charged when inside the POSS cages, providing little repulsive or attractive interactions, while polar CO provides significant repulsive interaction. In the case of water, the interaction energies are low because of hydrogen bonding between the water hydrogen atoms and the POSS oxygen atoms. The interaction energies of the absorbates at the center of T12 are typically smaller than for T10 due to the larger cavity size of T12. The Si5 face has the same basic structure for both T10 and T12 cages and, consequently, the interaction energies of the absorbate molecules at the face are similar. Interaction energies obtained using MP2 calculations are lower than those obtained from DFT calculations depending on the choice of the functional. For example, use of the ωB97XD functional that treats dispersion interactions more completely than the B3LYP functional, produces values closer to the MP2 values. These results, therefore, suggest that dispersion is important in the interaction between small molecules and POSS cages.

Spectroscopic signatures of the carbon buckyonions C60@C180 and C60@C240: a dispersion-corrected DFT study

We have investigated, using dispersion corrected DFT methods, the structure and the spectroscopic properties of carbon buckyonions C60@C180 and C60@C240. C60, C180 and C240 showed a noticeable variation of their geometries in C60@C180 and C60@C240, upon encapsulation. Inclusion of the dispersion correction term in the calculations has a significant effect on the geometry. C60@C180 has a large positive interaction energy, while for C60@C240 a negative value is found indicating that only C240 can easily accommodate C60. In both cases dispersion interactions strongly contribute to the stabilization of the complexes. Vibrational frequencies, electronic transitions and NMR properties have been computed. The results show that encapsulation leads to appreciable variation in the characteristic resonances thus offering a useful tool for a spectroscopic identification of these species.

Halogen Doping Effect on Electronic Structure of Poly(methylphenyl)silane: a Theoretical Study

In order to well understand the halogen (F2, Cl2, Br2, I2, ICl) doping effect on electronic structure of poly(methylphenyl)silane (PMPSi), a theoretical investigation on halogen doped models has been performed using density functional theory (DFT). The optimized structures of PMPSi are obtained at the BH&HLYP/6-31G* level, and the stagger conformation is the most stable conformation among three isomers. Halogen doped PMPSi were optimized at the BH&HLYP level based on the stagger conformation, and the changes of geometry parameters are compared for PMPSi and halogen doped PMPSi. Furthermore, frontier molecular orbital energies and electronic absorption spectra of halogen doped PMPSi are investigated. The results show that energy of the highest occupied molecular orbital (HOMO) almost keeps the same when PMPSi is doped by halogen, but energy of the lowest unoccupied molecular orbital (LUMO) becomes lower, the energy gap is therefore decreased according to the order Cl2>F2>ICl>Br2>I2. When PMPSi is doped by halogen, electron transition is assigned to the HOMO-1→LUMO, it leads to red shift of the absorption spectrum of complex, and presents relative strong absorption peak in visible region. Natural bond orbital (NBO) analyses were performed to study the charge distribution of halogen doped PMPSi, it is found that charge transfer from backbone to halogen in the complex. The interaction energies of all the complexes which were corrected for basis set superposition error (BSSE) are from -0.61 to -3.20 kcal/mol. The result what arouse most interest is, the higher polarity of dopant, the larger interaction energy of complex. In addition, the influence of position of dopant on energy gaps and interaction energies of all complexes is discussed in our present work. This study is expected to provide theoretical clues and foundation for future research on improving the photoelectric property of PMPSi.

Quantum Mechanical Design and Structures of Hexanuclear Sandwich Complex and Its Multidecker Sandwich Clusters (Li6)n([18]Annulene)n+1 (n = 1–3)

By means of density functional theory, a hexanuclear sandwich complex [18]annulene-Li6-[18]annulene which consists of a central Li6 hexagon ring and large face-capping ligands, [18]annulene, is designed and investigated. The large interaction energy and HOMO-LUMO gap suggest that this novel charge-separated complex is highly stable and may be experimentally synthesized. In addition, the stability found in the [18]annulene-Li6-[18]annulene complex extends to multidecker sandwich clusters (Li6)n([18]annulene)n+1 (n = 2-3). The energy gain upon addition of a [18]annulene-Li6 unit to (Li6)n-1([18]annulene)n is pretty large (96.97-98.22 kcal/mol), indicating that even larger multideckers will also be very stable. Similar to ferrocene, such a hexanuclear sandwich complex could be considered as a versatile building block to find potential applications in different areas of chemistry, such as nanoscience and material science.

Enhancement of Iodine–Hydride Interaction by Substitution and Cooperative Effects in NCX–NCI–HMY Complexes

The NCX-NCI-HMY (X=H, Cl, Br, I, Li; M=Be, Mg; Y=H, Li, Na) trimers are investigated to find ways to enhance the iodine-hydride interaction. The interaction energy in the NCI-HMH dimer is -2.87 and -5.87 kcal mol(-1) for M=Be and Mg, respectively. When the free H atom in the NCI-HMH dimer is replaced with an alkali atom, the interaction energy is enhanced greatly. When NCX is added into this dimer, the interaction energy of the iodine-hydride interaction is increased by 9-45 % and its increased percentage follows the order X=Cl<Br<H<I<Li and M=Be<Mg. The combination of the alkali substitution and the cooperativity results in a more prominent enhancing effect. The largest interaction energy is found for the NCLi-NCI-HMgLi trimer (-7.03 kcal mol(-1)). The influence of the I···H interaction on the X···N interaction is also studied in the trimers. Both types of interactions are analyzed with NBO, AIM, and MEP. The interaction energy in the trimer is also unveiled by a many-body analysis.

A quantum chemical calculation on Fe(CO)5 revealing the operation of the Dewar–Chatt–Duncanson model

A nonstandard computational scheme has been applied to calculate Fe(CO)(5) with the aim to illustrate the operation of the Dewar-Chatt-Duncanson model by computation. A full configuration interaction (CI) calculation in an active space has been performed. The active space is built from naturally localized molecular orbitals (NLMOs) localized in bond regions or forming lone pairs. For selecting this active space, Weinhold's perturbation theory formulated in the natural bond orbital (NBO) space has been applied. Bonding, lone pair, and antibond NBOs exhibiting large interaction energies serve to define the active space. The actually applied active space, however, comprises NLMOs that are close in shape to the NBOs indicated by perturbation theory. Thus, a CI calculation with localized orbitals has been performed meeting the classical reasoning of chemists that is often based on local bonding concepts. The computational scheme yields the Lewis structure for Fe(CO)(5) whose energy is identical to the Hartree-Fock energy. The Lewis energy comprises CO → Fe σ-electron transfer (ET) and CO ← Fe electron back donation (BD). This Lewis energy gets lowered by localized correlation energy contributions caused by ET processes where electrons are back donated from the Fe d-lone pairs into the CO ligands. Thus, electron correlation within the selected active space is dominated by electron BD. Energies and electron populations of the NBOs support the notion that electrons are preferentially back donated into the equatorial CO ligands. Weights of local Slater determinants, determining the correlation energy, also point to a predominant BD into the equatorial CO ligands. Correlation energy increments resulting from electron BD into single antibond orbitals of the CO ligands have been calculated. These energy quantities also demonstrate that BD into the equatorial CO ligands is more energy lowering than BD into the axial CO ligands.

Nonadditive effects on the stability of Be3: A benchmark CASSCF + averaged quadratic coupled cluster study of the equilateral and linear symmetrical configurations

AbstractThe optimized geometries and binding energies (BEs) for the linear and triangular isomers of the beryllium trimer have been recently studied through benchmark multireference averaged quadratic coupled clusters calculations using very large complete active space self‐consistent field (SCF). The largest augmented correlation‐consistent atomic basis set for Be was used (aug‐cc‐pV5Z). The BEs are 26.1 and 16.1 kcal/mol for the equilateral and linear isomers, and these were corrected to account for the basis set superposition errors (Amaro‐Estrada et al., J. Chem. Phys. 2011, 135, 104311). In the light of the very small (2.4 kcal/mol) BE of Be2, these large interaction energies for the trimers must be due to the nonadditive collective effects, which we set out to determine here using state‐of‐the‐art quantum chemical methods. The nonadditive three‐body corrections proved to be extremely large. In fact, their relative weight when divided by total BEs is about 94% for both isomers. We found that in this case, the two‐body and the three‐body terms go in the same direction, both contributing to the stabilization of the trimers, which yields the rather large BEs for both isomers. Considering that Be3 contains one trimer and three pairs, this would mean that for solid beryllium (where the total number of dimers and trimers become virtually the same), we may confirm the original assumption of Kolos et al. (Chem. Phys. Lett. 1976, 41, 431), to wit, that nonadditive effects for solid beryllium are conspicuously large. © 2012 Wiley Periodicals, Inc.

Enhancing the function, non-additivity, and substitution position effect of the Li atom in the cation–π interaction and its mechanism: an ab initio study of Li+ ··· Li-substituted benzene complexes

Quantum chemical calculations have been performed to study the cation–π interaction in the Li+ ··· C6H6– n Li n (n = 0–6) complex. The results show that the cation–π interaction is enhanced by lithium substitution in the aromatic ring. With increasing number of lithium substituents in the aromatic ring, the total interaction energy becomes more negative. However, the average contribution from one Li substituent to the interaction energy becomes smaller. The lithium substituent in the aromatic ring displays negative non-additivity in enhancing the cation–π interaction. The substitution position of the lithium substituent in the aromatic ring has a prominent effect on the strength of the cation–π interaction. The largest interaction energy (–97.7 kcal mol−1) is found for the Li+ ··· 1,3,5-C6H3Li3 complex. The enhancing effect of the Li atom can be understood in terms of the natural population analysis (NPA) charge on the carbon atom in the aromatic ring, the most negative electrostatic potential at the center of the aromatic ring, and energy decomposition.

Electronic properties of the halogen bonds Z3CX···Y− between halide anions and methyl halides

In this study, the linear halogen bonds Z3CX···Y– (X = Cl, Br; Y, Z = F, Cl, Br) are theoretically investigated. They have large interaction energies—23–160 kJ/mol, and the interactions are closed-shell in nature. In some systems, a blue-shifted halogen bond is formed. Although the electrostatic interaction is important, the intermolecular charge transfer caused by the intermolecular hyperconjugation n(Y−) → σ*(CX) and the intramolecular charge redistribution by the intramolecular hyperconjugation n(Z) → σ*(CX) play important roles in the formation of the halogen bonds.

The single-electron hydrogen, lithium, and halogen bonds with HBe, H2B, and H3C radicals as the electron donor: an ab initio study

Quantum chemical calculations have been performed for the complexes with HBe, H2B, and H3C radicals as the electron donors and with HF, LiF, and ClF as the electron acceptors. For HBe, H2B, and H3C radicals, the ability of donating electrons is dependent on the nature of the electron donor atom. In addition, it is also affected by the nature of the electron acceptor atom. A partially covalent bond is formed in HBe–Cl···F and H2B–Cl···F complexes, which exhibits a large interaction energy, short binding distance, large bond elongation, and big frequency shift. The complexes have also been analyzed with natural bond orbital and atoms in molecules.