GridMol is a “one-stop” platform for molecular modeling, scientific computing and molecular visualization aided by High Performance Computing Environment. GridMol version 2.0 emphatically introduces two unique features, the first is fragment-based linear scaling quantum chemistry methods, such as molecular fractionation with conjugate caps and fragment molecular orbital methods; the second is visualization of computational processes, such as structural optimization and intrinsic reaction coordinate calculation. Compared with version 1.0, fragment-based linear scaling quantum chemistry methods implemented in GridMol version 2.0 can be used as a useful tool for performing quantum calculations for large molecular systems to explore the mechanisms involved in protein–ligand or targeted-drug interactions.
The photocatalytic yield of the g-C3N4 for CO2 reduction was modified by phosphorus doping. The possible reaction pathways for CO2 reduction on the P-doped g-C3N4 (PCN) surface were investigated by DFT calculations for the first time. The experimental results showed that P doping improves the production of CH4 through the increase in the driving force of the electrons. The partial density of states of the PCN showed that the VBM and CBM are composed of px, py and s orbitals of the N atoms and pz states of carbon, nitrogen, and phosphorus, respectively and therefore, the P-doping increase carriers lifetime. Mechanism studies confirm that formic acid, formaldehyde, methanol and methane are the most probable products. The methane having positive adsorption energy can be easily desorbed from the PCN surface and the Gibbs activation energy of the final step is 1.98 eV. The formation of H2COOH is the rate-determining step.
The field of molecular magnetism has benefited from the fluid synergy between experimentalists and theoreticians for decades This has led to fundamental understanding of the processes that govern Single Molecule Magnets, allowing for the establishment of clear design criteria to control properties and the development of new synthetic methodologies, sophisticated magnetic measurements and innovative computational techniques. Herein we give an overview on the experimental and theoretical collaborative work we carried out as part of the synthesis group led by David Mills and the computational/theoretical team led by Nicholas Chilton at the University of Manchester. Together with this, we provide a perspective on collaborative work in molecular magnetism and how such collaborations are essential for advancing the field further.
We studied the ring opening of propylene oxide (PO) by salen-M coordinated OH- group [M = Al(Ⅲ), Sc(Ⅲ), Cr(Ⅲ), Mn(Ⅲ), Fe(Ⅲ), Co(Ⅱ), Co(Ⅲ), Ni(Ⅱ), Cu(Ⅱ), Zn(Ⅱ), Ru(Ⅲ) and Rh(Ⅲ)]. The results show that the ring opening energy barriers for M(II) complexes are much lower than those with M(III) complexes in the gas phase, and the barriers correlate linearly with the negative charges on the OH- group, the Fukui function condensed on the OH- group. The nucleophilicity ordering in gas phase can be rationalized by the ratio of formal positive charges/radius of M cations. Solvent effect greatly increases the barriers of M(II) complexes, but slightly changes the results of M(III) ones, making the barriers similar. Analysis indicates that the reaction heats are linearly proportional to the reverse reaction barriers. The relationships established here can be used to estimate the ring opening barriers and to screen epoxide ring opening catalysts.
We calculate the concerted pathway of 1, 2-bromochloroethane monocation to C2H4+ and BrCl using the Minnesota density functional M06-2X and the def2-TZVP basis set. We also calculate the elimination channel of 1, 2-bromochloroethane monocation to C2H4 and BrCl+ for the reason that positive charge can be assigned to either moiety in the fragmentation process of 1,2-C2H4BrCl+. Our results demonstrate that the elimination channel of 1, 2-bromochloroethane monocation to C2H4+ and BrCl is preferred, and the singly charged 1,2-bromochloroethane ions surpass two energy barriers and then separate into C2H4+ + BrCl by an asynchronous concerted process. Experimentally, we confirm that this elimination channel is from the dissociative ionization process of 1,2-bromochloroethane monocation by dc-slice imaging technique. Besides, we can see in laser-induced time-of-flight mass spectra of 1,2-bromochloroethane that fragment ion C2H4+ occur at the laser intensity of 6.0×1013 W/cm2 while BrCl+ occur at a higher laser intensity, which is consistent with the theoretical results that appearance energy of ion C2H4+ should be lower than that of BrCl+, and this is the reason why the low-velocity component of ion BrCl+ is absent from our sliced images.
Abstract: Searching for energetic materials with balanced detonation performance and sensitivity is the enduring ambition in the evolution of high energy density materials (HEDMs). The coplanar molecular structure of energetic compound has a powerful impact on performance. Herein, the novel compounds of bis(nitrotriazoles) tetrazine (BNTT) was designed and investigated by density functional theory(DFT) method. However, the coplanar BNTT’s oxides would a highlight of molecular design with good balance between superior performance with acceptable sensitivities. Results show that all these designed compounds possess high densities, positive heats of formation, remarkable detonation performance, and acceptable impact sensitivity. In particular, B1-3 possess higher density (ρ=1.97g·cm-3) and exhibits the better balance between detonation performance (Q=1779.83 cal·g-1, D=9.48km·s-1, P=42.01GPa) and sensitivity (h50%=28cm) than RDX. The theoretical study offer that all novel compounds possess acceptable sensitivity. It may be seen as the potential candidates of HEDMs.
Mechanism of the oxidative nonpolar inversion reaction catalyzed by N-heterocyclic carbenes (NHCs) to achieve benzoxazoles was investigated in very details. The reaction was revealed to occur through five processes, and for oxidation in the second process, two successive tautomerizations followed by oxidation were demonstrated to be more energetically favorable than the other two pathways. The rate-determining step was disclosed to be the oxidation by 3,3’-5,5’-tetra-tert-butyl-4,4’-diphenoquinone (DQ). Afterwards, mechanism calculations to the non-catalyzed reaction was conducted and it was revealed that the excessive exothermic property of the initial step should be the main reason for the extremely high barrier in the following step. While with participation of NHC, this unfavorable transformation can be deftly prevented according to the specific sequence and amount of reagents addition, and therefore to enable the reaction to occur under mild conditions.
Multi-reference configuration interaction, MR-CI (including extensivity corrections, named +Q) calculations have been performed on S0 to S3 states of cyclohexa-2,4-diene-1-thione (thione 24) and cyclohexa-2,5-diene-1-thione (thione 25), which are thione isomers of thiophenol. Several types of uncontracted MR-CIS and MR-CISD wavefunctions have been employed, comprising MR-CI expansions as large as ~ 374 x 106 configuration state functions. The nature of the studied excited states has been characterized. Vertical excitation energies (ΔE) and oscillator strengths (f) have been computed. The most intense transitions (S0→S2 for 24 and S0→S3 for 25) do not change with the wavefunction, although a variation as large as ~ 1 eV has been obtained for the S3 state of 24. On the other hand, ΔE changes at most ~ 0.15 eV for 25, as the wavefunction changes. The S1 state of both thiones has nπ* character and is in the visible region. For 24 S2 and S3 are ππ* and nπ* states, respectively, while for 25 the reverse order has been obtained. S2 and S3 are in the range from ~ 3.5 to 5.2 eV, at the highest level (MR-CI+Q). It is the first time that the excited states of the title molecules are studied. The computed results agree with the experimental onsets of photoreactions of thiones 24 and 25 found by Reva et. al. (Phys. Chem. Chem. Phys. 2015, 17, 4888).
Quantum chemical calculations are applied to study the complexes between X2TO (X=H, F, Cl, Br, CH3; T=C, Si, Ge, Sn) and CO2. The carbon atom of CO2 as a Lewis acid participates in the O•••C carbon bond, whereas its oxygen atom as a base engages in the O•••T tetrel bond with X2TO. Most of complexes are stabilized by a combination of both O•••C and O•••T interactions. The interaction energies are dependent on the nature of T and X atoms/groups. Both the electron-withdrawing halogen group and the electron-donating methyl group increase the interaction energy, up to 51 kJ/mol in F2SiO•••CO2. One F2SiO molecule can bind with different number of CO2 molecules from one to four; as the number of CO2 increases, the average interaction energy for each CO2 is decreased but it can contribute at least 27 kJ/mol stabilization energy. Therefore, silicon-containing molecules are good absorbents for CO2.
Boroxol (B3O3) rings and relevant hexagonal B3S3 structural blocks are ubiquitous in boron oxide/sulfide glasses, crystals, and high temperature liquids. However, the isolation of an ultimate heterocyclic B3O3 or B3S3 cluster in the free-standing form, with as few as six atoms, has been unsuccessful so far. We report on computational design of the simplest case of such a system: highly symmetric D3h B3S3+ (1A1) cluster. It is the well-defined global minimum on the potential energy surface, following global searches and electronic structure calculations at the B3LYP and single-point CCSD(T) levels. Chemical bonding analysis reveals an ideal system with skeleton Lewis B3S3 single bonds and unique double 6π/2σ aromaticity, which underlies its stability. The cluster turns out to be an inorganic analog of the 3,5-dehydrophenyl cation, a typical double π/σ aromatic system. It offers an example for chemical analogy between boron-based heterocyclic clusters and aromatic hydrocarbons. Double π/σ aromaticity is also a new concept in heterocyclic boron clusters. Prior systems such as borazine, boroxine, and boronyl boroxine only deal with π aromaticity as in benzene.
Experimental studies on the speciation of berkelium in carbonate media have shown that complexation of berkelium(III) by carbonate results in spontaneous oxidation to berkelium(IV) and that multiple species can be present in solution. We studied two proposed structures present in solution based on theoretical comparisons with spectroscopic data previously reported for Bk(IV) carbonate solutions. The multiconfigurational character of the ground and low-lying excited states in both complexes is demonstrated to result from the strong spin-orbit coupling. Although bonding in berkelium(IV) carbonate and carbonate-hydroxide complexes is dominated by strong Coulombic forces, the presence of the non-negligible covalent character is supported by ligand-field theory, natural localized orbitals and topological studies of the electron density. Bond orders based in natural localized molecular orbitals (NLMOs) show that Bk–OH bonds possess enhanced orbital overlap that is reflected in the bond strength.
Hydroxyl derivatives of cinnamic acid, both natural and synthetic, are well-known antioxidants. However, not all of them feature the same radical-scavenging propensity. Establishing the relation between structure and reactivity towards radical of those species plays a crucial role in the design of novel antioxidant pharmaceuticals founded on the same parent structure. The study aims at clarifying the relationship between topology, geometry, electron and spin density distribution and the radical-scavenging activity. Different mechanisms are discussed based on the enthalpies of the possible structures generated in the process of dissociation of the OH-bonds. All structures are modelled utilizing first principles methods and accounting for the polar medium at neutral pH (B3LYP/6-311++G**/PCM). A hybrid mechanism is suggested applicable not only to hydroxylated cinnamic acids but to phenolic acids in polar environment in general.
Models of surface enhancement of molecular electronic response properties are challenging for two reasons: (1) molecule-surface interactions require the simultaneous solution of the molecular and the surface dynamic response (a daunting task); (2) when solving for the electronic structure of the combined molecule+surface system, it is not trivial to single out the particular physical effects responsible for enhancement. To attack this problem, in this work we apply a formally exact decomposition of the system’s response function into subsystem contributions by employing subsystem DFT which grants access to dynamic polarizabilities and optical spectra. In order to access information about the interactions between the subsystems, we extend a previously developed subsystem-based adiabatic connection fluctuation-dissipation theorem of DFT to separate the additive from the nonadditive correlation energy and identify the nonadditive correlation as the van der Waals interactions. As an example, we choose benzene adsorbed on monolayer MoS2. We isolate the contributions to the benzene’s dynamic response arising from the interaction with the surface and for the first time, we evaluate the enhancements to the effective C6 coefficients as a function of benzene-MoS2 distance and adsorption site. We also quantify the spectral broadening of the benzene’s electronic excited states due to their interaction with the surface. We find that the broadening has a similar decay law with the molecule-surface distance as the leading van der Waals interactions (i.e., R-6) and that the surface enhancement of dispersion interactions between benzene molecules is less than 5\%, but still large enough (0.5 kcal/mol) to likely play a role in the prediction of interface morphologies.
The mechanisms of Cp*Rh(OAc)2-catalyzed coupling reaction of N-methoxybenzamide with alkyl-terminated enyne have been investigated by density functional theory (DFT) calculations. With the addition of NaOAc and changing solvent, the product transforms from lactam P1 in reaction A to iminolactone P2 in reaction B, due to the formed stable OAc- coordinated intermediate. The electronic effect and steric effect account for the observed regioselectivity in reaction B collectively.
The transformation mechanism and kinetics of 2-chloro-1,1,2-trifluoroethyl-difluoromethyl-ether (CTDE, CHF2OCF2CHFCl) triggered by OH radicals were researched by DFT methods and canonical variational transition state theory. The computational rate constant including small-curvature tunneling correction was in commendable agreement with the experimental data. Two hydrogen abstraction channels to form the alkyl radicals of C·F2OCF2CHFCl and CHF2OCF2C·FCl were observed, and the formation of CHF2OCF2C·FCl was more favorable than C·F2OCF2CHFCl in kinetics and thermodynamics. Subsequent evolution of CHF2OCF2C·FCl in the presence of NO and O2 indicated that the organic nitrate (CHF2OCF2CONO2FCl) was the stable product. The dechlorinate of alkoxy radical (CHF2OCF2C(O·)FCl) was the most favorable degradation channel and the estimated ozone depletion potential for CTDE relative to CFC-11 was 0.0204, which could lead to a consequence of ozone depletion. Computed atmospheric lifetime for CTDE was 3.69 years by considering the combined contributions from OH radicals and Cl atoms. The total radiative forcing and global warming potential of CTDE were respectively 0.547 W m-2 ppbv and 628.58 (100 years) at 298 K, suggesting that the contribution of CTDE to the greenhouse effect is moderate.
Introduction of a heterocyclic ring and an amino-ethyl-amino group to D-A type photosensitive dyes can modulate the lifetime of the charge separation generated in the D-A dyes as well as their electronic and UV-Vis absorption properties. Here we performed DFT and TDDFT calculations to study eleven derivatives of a triphenylamine-pyrimidine, MTPA-Pyc, in order to improve the performance of MTPA-Pyc as solar cell sensitizers. Five heterocyclic rings and an amino-ethyl-amino group were introduced on the styryl moiety of MTPA-Pyc. The results show that introduction of heterocyclic rings generally causes an absorption red-shift, but absorption intensity is reduced due to the increase of dihedral angle between the donor and acceptor. Further introduction of an amino-ethyl-amino group to these dyes with a heterocyclic ring modification disrupts the conjugation between donor and acceptor, which does not benefit the absorption but may have potential to increase the lifetime of charge separation of the dyes. This work identified two out of eleven dyes that have the best potential for solar cell applications.
Time-dependent density functional theory approach implemented at hybrid-B3LYP, GGA-PBE and DFTB levels of theory was used to model photoinjection in organic-dye/TiO2 quantum-dot to explore the prospects of improvement of DSSC. The photosensitizer used in this study consisted of six carbazole based organic dyes having acceptor as cyanoacrilic acid group and oligothiophene π-bridge spacer. The modifications were made in the dyes by increasing length of the spacer by adding thiophene and oxadiazole rings at different positions of the donor-acceptor bridge. The structural variations appeared to alter the electronic and optical properties of dyes studied via energy levels and excitation spectra. The UV-Vis spectra calculated for all the dyes in solvents exhibited a red shift in spectral peaks with increase in polarity of the solvents. The findings of the study pointed towards photoinjection of indirect nature studied in dye-(TiO2)96 complex for six different dyes. The substitution of oxadiazole ring in center and addition of a thiophene ring at the edge of the spacer produced two dyes which exhibited lowest injection energies of 0.11eV and 0.17 eV along with the regeneration energies of 1.18 eV and 1.12 eV respectively. The dyes reported herein may have promising applications in photoanode for enhancing the performance of DSSC.
In this paper, the Shannon entropy and Fisher information are studied for the screened Kratzer potential model (SKP). We calculated the position and momentum entropies for the screened Kratzer potential for its ground states as well as the first excited state. Our result shows that the sum of the position and momentum entropies satisfies the lower bound Berkner, Bialynicki–Birula and Mycieslki (BBM) inequality. Also, our results showed that decreasing Shannon entropy in the position space was complemented with an increasing Shannon entropy in the momentum space. Similarly, we evaluated for Fisher information and show that the Stam, Cramer-Rao inequalities are satisfied. The squeezing phenomena were also observed for certain values of the screening parameter α.