The effects of external electric field: creating non-zero first hyperpolarizability for centrosymmetric benzene and strongly enhancing first hyperpolarizability for non-centrosymmetric edge-modified graphene ribbon H2N-(3,3)ZGNR-NO2.

How to generate a non-zero first hyperpolarizability for a centrosymmetric molecule is a challenging question. In this paper, an external (pump) electric field is used to make a centrosymmetric benzene molecule generate a non-zero value of the electric field induced first hyperpolarizability (β (F) ). This comes from the centrosymmetry breaking of electron cloud.

The effects of the formation of Stone-Wales defects on the electronic and magnetic properties of silicon carbide nanoribbons: a first-principles investigation.

Detailed first-principles density functional theory (DFT) computations were performed to investigate the geometries, the electronic, and the magnetic properties of both armchair-edged silicon carbide nanoribbons (aSiCNRs) and zigzag-edged silicon carbide nanoribbons (zSiCNRs) with Stone-Wales (SW) defects. SW defects in the center of aSiCNRs can remarkably reduce their band gaps, irrespective of the orientation of the defect, whereas zSiCNRs with SW defects in the center or at the edges exhibit degenerate energies of their ferromagnetic (FM) and antiferromagnetic (AFM) states, in which metallic and half-metallic behavior can be observed, respectively; half-metallic behavior can even be observed in both the FM and AFM states simultaneously. Further, it was shown that the formation energies of the SW defects in SiCNRs are orientation dependent, and the formation of edge defects is always favored over the formation of interior defects in zSiCNRs.

Influence of C-terminal tail deletion on structure and stability of hyperthermophile Sulfolobus tokodaii RNase HI.

The C-terminus tail (G144-T149) of the hyperthermophile Sulfolobus tokodaii (Sto-RNase HI) plays an important role in this protein's hyperstabilization and may therefore be a good protein stability tag. Detailed understanding of the structural and dynamic effects of C-terminus tail deletion is required for gaining insights into the thermal stability mechanism of Sto-RNase HI. Focused on Sulfolobus tokodaii RNase HI (Sto-RNase HI) and its derivative lacking the C-terminal tail (ΔC6 Sto-RNase HI) (PDB codes: 2EHG and 3ALY), we applied molecular dynamics (MD) simulations at four different temperatures (300, 375, 475, and 500 K) to examine the effect of the C-terminal tail on the hyperstabilization of Sto-RNase HI and to investigate the unfolding process of Sto-RNase HI and ΔC6 Sto-RNase HI.

New acceptor-bridge-donor strategy for enhancing NLO response with long-range excess electron transfer from the NH2...M/M3O donor (M = Li, Na, K) to inside the electron hole cage C20F19 acceptor through the unusual σ chain bridge (CH2)4.

Using the strong electron hole cage C20F19 acceptor, the NH2...

Structural and dynamic basis of human cytochrome P450 7B1: a survey of substrate selectivity and major active site access channels.

Cytochrome P450 (CYP) 7B1 is a steroid cytochrome P450 7α-hydroxylase that has been linked directly with bile salt synthesis and hereditary spastic paraplegia type 5 (SPG5). The enzyme provides the primary metabolic route for neurosteroids dehydroepiandrosterone (DHEA), cholesterol derivatives 25-hydroxycholesterol (25-HOChol), and other steroids such as 5α-androstane-3β,17β-diol (anediol), and 5α-androstene-3β,17β-diol (enediol). A series of investigations including homology modeling, molecular dynamics (MD), and automatic docking, combined with the results of previous experimental site-directed mutagenesis studies and access channels analysis, have identified the structural features relevant to the substrate selectivity of CYP7B1.

Direct ab initio study on the rate constants of radical C2(A 3Π(u)) + C3H8 reaction.

The mechanism and kinetics of the radical (3)C(2) + C(3)H(8) reaction have been investigated theoretically by direct ab initio kinetics over a wide temperature range. The potential energy surfaces have been constructed at the CCSD(T)/B3//UMP2/B1 levels of theory. The electron transfer was also analyzed by quasi-restricted orbital (QRO) in detail.

Influence of hyperthermophilic protein Cren7 on the stability and conformation of DNA: insights from molecular dynamics simulation and free energy analysis.

Cren7, a novel chromatin protein highly conserved among crenarchaea, plays an important role in genome packaging and gene regulation. However, the detail dynamical structural characteristic of the Cren7-DNA complex and the detail study of the DNA in the complex have not been done. Focused on two specific Cren7-DNA complexes (PDB codes 3LWH and 3LWI ), we applied molecular dynamics (MD) simulations at four different temperatures (300, 350, 400, and 450 K) and the molecular mechanics Poisson-Boltzmann surface area (MM-PBSA) free energy calculation at 300 and 350 K to examine the role of Cren7 protein in enhancing the stability of DNA duplexes via protein-DNA interactions, and to study the structural transition in DNA.

Insights into the thermal stabilization and conformational transitions of DNA by hyperthermophile protein Sso7d: molecular dynamics simulations and MM-PBSA analysis.

In the assembly of DNA-protein complex, the DNA kinking plays an important role in nucleoprotein structures and gene regulation. Molecular dynamics (MD) simulations were performed on specific protein-DNA complexes in this study to investigate the stability and structural transitions of DNA depending on temperature. Furthermore, we introduced the molecular mechanics/Poisson-Boltzmann surface area (MM-PBSA) approach to analyze the interactions between DNA and protein in hyperthermophile.

Mechanism insights of ethane C-H bond activations by bare [Fe(III)═O]+: explicit electronic structure analysis.

Alkane C-H bond activation by various catalysts and enzymes has attracted considerable attention recently, but many issues are still unanswered. The conversion of ethane to ethanol and ethene by bare [Fe(III)═O](+) has been explored using density functional theory and coupled-cluster method comprehensively. Two possible reaction mechanisms are available for the entire reaction, the direct H-abstraction mechanism and the concerted mechanism.

Ab initio investigation on ion-associated species and association process in aqueous Na2SO4 and Na2SO4/MgSO4 solutions.

In the present paper, the possible ion associated species in pure Na(2)SO(4) and mixed Na(2)SO(4)/MgSO(4) aqueous solutions are investigated via the ab initio method at the HF/6-31+G∗ level. The vibrational v(1)-SO(4)(2-) band is analyzed. For the unhydrated species, when the number of metal ions around the SO(4)(2-) ion is less than 3, the dominating effect to the v(1)-SO(4)(2-) band is the polarization of the cations, while the M-O bonding will be dominating as the number is equal to or more than 3.

Alkali metal atom-aromatic ring: a novel interaction mode realizes large first hyperpolarizabilities of M@AR (M=Li, Na, and K, AR=pyrrole, indole, thiophene, and benzene).

Several new electride compounds M@pyrrole (M = Li, Na, and K), Li@AR (AR = indole, thiophene, and benzene), Li@tryptophan and Li@serotonin were designed and investigated, which exhibit considerably large first hyperpolarizabilities (β(0)) (6705, 1116, 11399, 5781, 4808, 1536, 8106, and 9389 au, respectively) by comparison with their corresponding sole molecules pyrrole (β(0) = 30 au), indole (104 au), thiophene (6 au), benzene (0 au), tryptophan (159 au) and serotonin (151 au), respectively. The computational results revealed that the interaction of the alkali metal atom with π-conjugated aromatic ring (AR) is one effectively new approach to produce diffuse excess electron to get a large β(0) value, which is advantageous for the design of the novel high-performance NLO materials with π-conjugated AR: alkali metal atoms doped nanomaterials and biomolecules.

Evolution of lone pair of excess electrons inside molecular cages with the deformation of the cage in e2@C60F60 systems.

For unusual e(2)@C(60)F(60)(I(h), D(6h), and D(5d)) cage structures with two excess electrons, it is reported that not only the lone pair in singlet state but also two single excess electrons in triplet state can be encapsulated inside the C(60)F(60) cages to form single molecular solvated dielectrons. The interesting relationship between the shape of the cage and the spin state of the system has revealed that ground states are singlet state for spherical shaped e(2)@C(60)F(60)(I(h)) and triplet states for short capsular shaped e(2)@C(60)F(60)(D(6h)) and long capsular shaped e(2)@C(60)F(60)(D(5d)), which shows a spin evolution from the singlet to triplet state with the deformation of the cage from spherical to capsular shape. For these excess electron systems, the three ground state structures have large vertical electron detachment energies (VDEs (I) of 1.

Direct ab initio dynamics study of radical C4H (X̃2Σ+) + CH4 reaction.

The methane (CH(4)) hydrogen abstraction reaction by linear butadiynyl radical C(4)H (CCCCH) has been investigated by direct ab initio dynamics over a wide temperature range of 100-3000 K, theoretically. The potential energy surfaces (PESs) have been constructed at the CCSD(T)/aug-cc-pVTZ//BB1K/6-311G(d,p) levels of theory. Two different hydrogen abstraction channels by C(1) and C(4) of C(4)H (C(1)C(2)C(3)C(4)H) have been considered.

Theoretical mechanistic study of the reaction of the methylidyne radical with methylacetylene.

A detailed doublet potential energy surface for the reaction of CH with CH(3)CCH is investigated at the B3LYP/6-311G(d,p) and G3B3 (single-point) levels. Various possible reaction pathways are probed. It is shown that the reaction is initiated by the addition of CH to the terminal C atom of CH(3)CCH, forming CH(3)CCHCH 1 (1a,1b).

Exceptionally large second-order nonlinear optical response in donor-graphene nanoribbon-acceptor systems.

Graphene nanoribbon (GNR) has been used, for the first time, as an excellent conjugated bridge in a donor-conjugated bridge-acceptor (D-B-A) framework to design high-performance second-order nonlinear optical materials. Owing to the unique diradical planar conjugated bridge of GNR, D(NH(2))-GNR-A(NO(2)) exhibits exceptionally large static first hyperpolarizability (β(0)) up to 2.5×10(6) a.

Electric field-driven acid-base chemistry: proton transfer from acid (HCl) to base (NH3/H2O).

It is well-known that single H3N-HCl and H2O-HCl acid-base pairs do not react to form the ion pairs, H4N(+)Cl(-) and H3O(+)Cl(-), in isolation. On the basis of ab initio method, we propose a physical method of external electric field (Eext) to drive the proton transfer from acid (HCl) to base (NH3/H2O). Our results show that when Eext along the proton-transfer direction achieves or exceeds the critical electric field (Ec), the proton transfer occurs, such as, the Ec values of proton transfer for H3N-HCl and H2O-HCl are 54 × 10(-4) and 210 × 10(-4) au, respectively.

Beryllium and boron decoration forms planar tetracoordinate carbon strips at the edge of graphene nanoribbons.

Graphene has been viewed as one of the most promising materials in many fields. Recently, it has been found that by using Cu-decoration at the edge of zigzag graphene nanoribbons (ZGNR), a novel kind of planar tetracoordinate carbon (ptC) strip can be formed. In this paper, we investigate the edge-decoration of armchair graphene nanoribbons (AGNR) by various atom types and find that two new kinds of ptC strip can be effectively formed by using Be or B decoration.

Theoretical investigation of the interaction between carbon monoxide and carbon nanotubes with single-vacancy defects.

Density functional theory calculations are used to study the healing process of a defective CNT (i.e. (8,0) CNT) by CO molecules.

How does a double-cage single molecule confine an excess electron? Unusual intercage excess electron transfer transition.

To realize the chemistry of a multicage organic molecule with excess electron, as a model, by confining an excess electron inside a double-cage single molecule, the structures of e⁻@C₂₄F₂₂(NH)₂C₂₀F₁₈ (e⁻@AB) and e⁻@C₂₀F₁₈(NH)₂C₂₀F₁₈ (e⁻@BB') are obtained at the B3LYP/6-31G(d) + 4s4p theory level. It is confirmed that the excess electron is mainly confined inside one cage with larger interior electronic attractive potential (A for e⁻@AB and B for e⁻@BB') in the ground state, while the electron is localized in the other one in the first excited state. Owing to such excess electron localizations, an interesting intercage excess electron transfer transition takes places.

Reaction mechanism of CH + C(3)H(6): a theoretical study.

A detailed theoretical study is performed at the B3LYP/6-311G(d,p) and G3B3 (single-point) levels as an attempt to explore the reaction mechanism of CH with C(3)H(6). It is shown that the barrierless association of CH with C(3)H(6) forms two energy-rich isomers CH(3)-cCHCHCH(2) (1), and CH(2)CH(2)CHCH(2) (4). Isomers 1 and 4 are predicted to undergo subsequent isomerization and dissociation steps leading to ten dissociation products P(1) (CH(3)-cCHCHCH + H), P(2) (CH(3)-cCCHCH(2) + H), P(3) (cCHCHCH(2) + CH(3)), P(4) (CH(3)CHCCH(2) + H), P(5) (cis-CH(2)CHCHCH(2) + H), P(6) (trans-CH(2)CHCHCH(2) + H), P(7) (C(2)H(4) + C(2)H(3)), P(8) (CH(3)CCH + CH(3)), P(9) (CH(3)CCCH(3) + H) and P(12) (CH(2)CCH(2) + CH(3)), which are thermodynamically and kinetically possible.

Push-pull electron effects of the complexant in a Li atom doped molecule with electride character: a new strategy to enhance the first hyperpolarizability.

Differing from the reported strategy of push or pull electron effects of the complexant, a new strategy of the combination effects of both push and pull electrons of the complexant to enhance the first hyperpolarizability is performed with two Li atom doped complexants with a pair of difluorophenyl subunit rings. Large variance of the static first hyperpolarizabilities (beta(0)) are exhibited at the MP2/6-311++G(d,p) level. The order of the beta(0) values is 2.

CASSCF/CASPT2 calculation of the low-lying electronic states of the CH3Se neutral radical and its cation.

Electronic states of the CH(3)Se and its cation CH(3)Se(+) have been studied using the complete active space self-consistent field (CASSCF) and multiconfiguration second-order perturbation theory (CASPT2) methods in conjunction with the ANO-RCC(TZP) basis set. To investigate the Jahn-Teller effect on the CH(3)Se radical, C(s) symmetry was used for CH(3)Se in calculations. The results show that the Jahn-Teller effect is very small (69 cm(-1)) and the 1(2)A' state is slightly more stable than the 1(2)A'' state (8 cm(-1)).

Möbius basket molecule: structure and properties.

Expanding the non-knot region of the famous Möbius strip with topological one-sided characteristics, an interesting structure of a Möbius basket molecule with all real frequencies was obtained at the B3LYP/6-31G(d) level for the first time. This structure contains six fused five-membered pyrrole rings contrasting with the isolated pentagon rule for the fullerenes. The twisted handle joints the outer and inner surfaces of the bowl to form a one-sided container molecule.

Theoretical investigation on the origin of yellow-green firefly bioluminescence by time-dependent density functional theory.

The question whether the emitter of yellow-green firefly bioluminescence is the enol or keto-constrained form of oxyluciferin (OxyLH(2)) still has no definitive answer from experiment or theory. In this study, Arg220, His247, adenosine monophosphate (AMP), Water324, Phe249, Gly343, and Ser349, which make the dominant contributions to color tuning of the fluorescence, are selected to simulate the luciferase (Luc) environment and thus elucidate the origin of firefly bioluminescence. Their respective and compositive effects on OxyLH(2) are considered and the electronic absorption and emission spectra are investigated with B3LYP, B3PW91, and PBE1KCIS methods.

A theoretical study of the low-lying electronic states of the AlCCH radical and its ions.

The AlCCH radical is a photolysis product of the aluminum-acetylene adducts and has been considered as a molecule with potential interest in astrophysics. In this study, the low-lying electronic states of the AlCCH radical, cation, and anion have been studied by using complete active space self-consistent field and multiconfigurational second-order perturbation theory. The geometrical parameters, electron configurations, excitation energies, oscillator strengths, and harmonic vibrational frequencies are calculated in C(S) symmetry.