Accurate prediction of vertical electronic transitions of Ni(II) coordination compounds via time dependent density functional theory

Time dependent density functional theory calculations are completed for five Ni(II) complexes formed by polydentate peptides to predict the electronic absorption spectrum. The ligands examined were glycyl‐glycyl‐glycine (GGG), glycyl‐glycyl‐glycyl‐glycine (GGGG), glycyl‐glycyl‐histidine (GGH), glycyl‐glycyl‐cysteine (GGC), and triethylenetetramine (trien). Fifteen functionals and two basis sets were tested. On the basis of the mean absolute percent deviation (MAPD), the ranking among the functionals is: HSE06 ∼ MPW1PW91 ∼ PBE0 > ω‐B97x‐D ∼ B3P86 ∼ B3LYP ∼ CAM‐B3LYP > PBE ∼ BLYP ∼ BP86 > TPSS > TPSSh > BHandHLYP > M06 ≫ M06‐2X. Concerning the basis sets, the triple‐ζ def2‐TZVP performs better than the double‐ζ LANL2DZ. With the functional HSE06 and basis set def2‐TZVP the MAPD with respect to the experimental λ_max is 1.65% with a standard deviation of 1.26%. The absorption electronic spectra were interpreted in terms of vertical excitations between occupied and virtual MOs based on Ni‐d atomic orbitals. The electronic structure of the Ni(II) species is also discussed.     

Predicting a New Δ-Proton Sponge-Base of 4,12-Dihydrogen-4,8,12-triazatriangulene through Proton Affinity,Aromatic Stabilization Energy,and Aromatic Magnetism

Herein, we report designing a new Δ (delta-shaped) proton sponge base of 4,12-dihydrogen-4,8,12-triazatriangulene (compound 1 ) and calculating its proton affinity (PA), aromatic stabilization, natural bond orbital (NBO), electron density ρ(r), Laplacian of electron density ∇²ρ(r), (2D-3D) multidimensional off-nucleus magnetic shielding (σ_zz(r) and σ_iso(r)), and scanning nucleus-independent chemical shift (NICS_zz and NICS). Density functional theory (DFT) at B3LYP/6-311+G(d,p), ωB97XD/6-311+G(d,p), and PW91/def2TZVP were used to compute the magnetic shielding variables. In addition, relevant bases like pyridine, quinoline, and acridine were also studied and compared. The protonation of compound 1 yields a highly symmetric carbocation of three Hückel benzenic rings. Comparing our findings of the studied molecules showed that compound 1 precedes others in PA, aromatic isomerization stabilization energy, and basicity. Therefore, the basicity may be enhanced when a conjugate acid gains higher aromatic features than its unprotonated base. Both multidimensional σ_zz(r) and σ_iso(r) off-nucleus magnetic shieldings outperformed electron-based techniques and can visually monitor changes in aromaticity that occur by protonation. The B3LYP/6-311+G(d,p), ωB97XD/6-311+G(d,p), and PW91/def2TZVP levels showed no significant differences in detailing isochemical shielding surfaces.     

Stacking of Metal Chelates with Benzene: Can Dispersion‐Corrected DFT Be Used to Calculate Organic–Inorganic Stacking?

CCSD(T)/CBS energies for stacking of nickel and copper chelates are calculated and used as benchmark data for evaluating the performance of dispersion‐corrected density functionals for calculating the interaction energies. The best functionals for modeling the stacking of benzene with the nickel chelate are M06HF‐D3 with the def2‐TZVP basis set, and B3LYP‐D3 with either def2‐TZVP or aug‐cc‐pVDZ basis set, whereas for copper chelate the PBE0‐D3 with def2‐TZVP basis set yielded the best results. M06L‐D3 with aug‐cc‐pVDZ gives satisfying results for both chelates. Most of the tested dispersion‐corrected density functionals do not reproduce the benchmark data for stacking of benzene with both nickel (no unpaired electrons) and copper chelate (one unpaired electron), whereas a number of these functionals perform well for interactions of organic molecules.     

How computational methods and relativistic effects influence the study of chemical reactions involving Ru‐NO complexes?

Two treatments of relativistic effects, namely effective core potentials (ECP) and all‐electron scalar relativistic effects (DKH2), are used to obtain geometries and chemical reaction energies for a series of ruthenium complexes in B3LYP/def2‐TZVP calculations. Specifically, the reaction energies of reduction ( A ‐ F ), isomerization ( G‐I ), and Cl⁻ negative trans influence in relation to NH₃ ( J ‐ L ) are considered. The ECP and DKH2 approaches provided geometric parameters close to experimental data and the same ordering for energy changes of reactions A ‐ L . From geometries optimized with ECP, the electronic energies are also determined by means of the same ECP and basis set combined with the computational methods: MP2, M06, BP86, and its derivatives, so as B2PLYP, LC‐wPBE, and CCSD(T) (reference method). For reactions A ‐ I , B2PLYP provides the best agreement with CCSD(T) results. Additionally, B3LYP gave the smallest error for the energies of reactions J ‐ L . © 2017 Wiley Periodicals, Inc.     

An Unusal Case of Facile Non‐Degenerate P?C Bond Making and Breaking

Oxidation of Li/X phosphinidenoid complex 2 , obtained via selective deprotonation from the P‐H precursor 1 , with [Ph₃C]BF₄ led to the formation of two P‐F substituted diorganophosphane complexes 6 , 7 ; the latter tautomer 7 formed via H‐shift from 6 . In contrast, oxidation of 2 with [(p‐Tol)₃C]BF₄ led to three major and one minor intermediates at low temperature, which we tentatively assign to two pairs of P‐C atropisomers 10a , a′ and 10c , c′ and which differ by the relative orientations of their CH(SiMe₃)₂ and W(CO)₅ groups. Conversion of all isomers led finally to complex 11 having a ligand with a long P? C bond to the central trityl* carbon atom, firmly established by single‐crystal X‐ray analysis. DFT calculations at the B3LYP/def2‐TZVPP//BP86/def2‐TZVP level of theory on real molecular entities revealed the structures of the in situ formed combined singlet diradicals ( 4 + 5 and 5 + 9 ) and the nature of intermediates on the way to the final product, complex 11 . Remarkable is that all isomers of 11 possess relative energies in the narrow energy regime of about 20 kcal mol^?1. A preliminary study revealed that complex 11 undergoes selective P? C bond cleavage at 75 °C in toluene solution.     

Mechanism of the Thermal Z⇌E Isomerization of a Stable Silene; Experiment and Theory

The E and Z geometric isomers of a stable silene (tBu₂MeSi)(tBuMe₂Si)Si=CH(1‐Ad) ( 1 ) were synthesized and characterized spectroscopically. The thermal Z to E isomerization of 1 was studied both experimentally and computationally using DFT methods. The measured activation parameters for the 1Z ? 1E isomerization are: E_a=24.4 kcal mol^?1, ΔH^≠=23.7 kcal mol^?1, ΔS^≠=?13.2 e.u. Based on comparison of the experimental and DFT calculated (at BP86‐D3BJ/def2‐TZVP(‐f)//BP86‐D3BJ/def2‐TZVP(‐f)) activation parameters, the Z?E isomerization of 1 proceeds through an unusual (unprecedented for alkenes) migration–rotation–migration mechanism (via a silylene intermediate), rather than through the classic rotation mechanism common for alkenes.     

Quantum chemical study of the coordination of glycolic acid conformers and their conjugate bases to [Ca(OH2)n] (n=0–4) ions

A detailed exploration of the configurational and conformational space of glycolic acid and their conjugate bases has been carried out with the aid of first principles quantum chemical techniques at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p) levels of theory. The most stable configuration among the eight possible glycolic acid conformers corresponds to the E-s-cis, s-trans configuration, while the highest energy E-s-trans, s-cis conformer was found at 10.88 and 12.17 kcal mol⁻¹ higher in energy at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p) levels of theory, respectively. Upon dissociation of glycolic acid the s-cis(syn), and s-trans(anti) configurations of the glycolate anion can be formed. The anti conformer was found to be less stable than the syn one by 14.20 and 16.87 kcal mol⁻¹ at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p)) levels of theory, respectively. The computed B3LYP/6-311+G(d,p) proton affinity of the syn conformer for the protonation process affording the more stable E-s-cis, s-trans conformer, in vacuum was found to be 325.35 kcal mol⁻¹ (ΔG⁰ value). From a methodological point of view, our results confirm the reliability of the integrated computational tool formed by the B3LYP density functional model. This model has subsequently been used to investigate the interaction of Ca²⁺ ions with the glycolic acid conformers and their conjugate bases in vacuum and in the presence of extra water ligands. For the complexes of glycolic acid conformers the η²–O,O–(COOH) coordination, that is the structure that arises from the coordination of the Ca²⁺ to the carboxylic group, is the global minimum of the PES, while the η²–O(OH),O–(COOH) coordination is a local minimum found at only 1.0 and 1.3 kcal mol⁻¹ higher in energy at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p) levels of theory, respectively. Moreover, the two isomers exhibit nearly the same binding affinities, which are predicted to be 89 and 85 kcal mol⁻¹ at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p) levels of theory, respectively. The same holds also true for the complexes of the glycolate anion. The η²–O,O–(COO⁻) coordination involving the syn conformer of the glycolato ligand, is the global minimum, while the η²–O(OH),O–(COO⁻) one lies at 1.5 and 5.6 kcal mol⁻¹ higher in energy at the B3LYP/6-311+G(d,p) and CCSD(T)/6-31G(d,p) levels of theory, respectively. The other conformer with an η²–O,O–(COO⁻) coordination involving the anti conformer of the glycolato ligand, is less stable by only 0.2 kcal mol⁻¹ at both levels of theory. Noteworthy is the trend seen for the incremental binding energy due to the successive addition of water molecules to [HOCH₂C(O)O]Ca²⁺ species; the computed values are 30.4, 26.8, 22.9 and 16.2 kcal mol⁻¹ at the B3LYP/6-311+G(d,p) level of theory for the mono-, di-, tri- and tetraaqua complexes, respectively. This trend arising from the repulsion of the dipoles between the water ligands and from unfavorable many body interactions is in accordance with those anticipated from electrostatic considerations. The Ca(II)-water interaction weakens with increasing coordination of the metal. Obviously, it is the electrostatic nature of the Ca(II)-water interactions that accounts well for the computed coordination geometries of the cationic (aqua)(glycolato)calcium complexes. Calculated structures, relative stability and bonding properties of the conformers and their complexes with [Ca(OH₂)_n]²⁺ (n=0–4) ions are discussed with respect to computed electronic and spectroscopic properties, such as charge density distribution, harmonic vibrational frequencies and NMR chemical shifts.     

Synthesis and characterization of Ni(II) complexes bearing of 2‐(1H–benzimidazol‐2‐yl)‐phenol derivatives as highly active catalysts for ethylene oligomerization

Novel Ni(II) complexes of 2‐(1H–benzimidazol‐2‐yl)‐phenol derivatives (HL_x: x  =  1–5; C1–C5 ) have been synthesized and characterized. In the mononuclear complexes, the ligands were coordinated as bidentate, via one imine nitrogen and the phenolate oxygen atoms. The structures of the compounds were confirmed on the basis of FT‐IR, UV–Vis, ¹H‐, ¹³C–NMR, inductively coupled plasma and elemental analyses (C, H and N). The purity of these compounds was ascertained by melting point (m.p.) and thin‐layer chromatography. The geometry optimization and vibrational frequency calculations of the compounds were performed using Gaussian 09 program with B3LYP/TZVP level of theory. All Ni(II) complexes were activated with diethylaluminum chloride (Et₂AlCl), so that C2 showed the highest activity [6600 kg mol^?1 (Ni) h^?1], where the ligand contains a chlorine substituent. Oligomers obtained from the complexes consist mainly of dimer and trimer, and also exhibit high selectivity for linear 1‐butene and 1‐hexene. Both the steric and electronic effects of coordinative ligands affect the catalytic activity and the properties of the catalytic products.     

Comparison of density functionals for the study of the high spin low spin gap in Fe(III) spin crossover complexes

A detailed investigation of the accuracy of different quantum mechanical methods for the study of iron(III) spin crossover complexes is presented. The energy spin state gap between the high and low spin states; ΔE (HS‐LS) of nine iron(III) quinolylsalicylaldiminate complexes were calculated with nine different DFT functionals, then compared. DFT functionals: B3LYP, B3LYP‐D3, B3LYP*, BH&HLYP, BP86, OLYP, OPBE, M06L, and TPSSh were tested with six basis sets: 3‐21G*, dgdzvp, 6‐31G**, cc‐pVDZ, Def2TZVP, and cc‐pVTZ. The cations from the X‐ray crystal structures of [Fe(qsal‐OMe)₂]Cl·MeCN·H₂O, [Fe(qsal‐OMe)₂]Cl·2MeOH·0.5H₂O, [Fe(qsal‐OMe)₂]BF₄·MeOH, [Fe(qsal‐OMe)₂]NCS·CH₂Cl₂, [Fe(qsal‐F)₂]NCS, [Fe(qsal‐Cl)₂]NCS·MeOH, [Fe(qsal‐Br)₂]NCS·MeOH, [Fe(qsal‐I)₂]OTf·MeOH, and [Fe(qsal)₂]NCS?CH₂Cl₂ were used as starting structures. The results show that B3LYP, B3LYP‐D3, OLYP, and OPBE with a 6‐31G**, Def2TZVP, and cc‐pVTZ basis set give reasonable results of ΔE (HS‐LS) compared with the experimental data. The enthalpy of [Fe(qsal‐I)₂]⁺ calculated with an OLYP functional and cc‐pVTZ basis set (1.48 kcal/mol) most closely matches the experimental data (1.34 kcal/mol). B3LYP* yields an enthalpy of 5.92 kcal/mol suggesting it may be unsuitable for these Fe(III) complexes, mirroring recent results by Kepp (Inorg . Chem ., 2016, 55 , 2717–2727).     

Cyclic (Aryl)(Amido)Carbenes: NHCs with Triplet‐like Reactivity

The synthesis and study of a library of cyclic (aryl)(amido)carbenes (CArAmCs), which represent a class of electrophilic NHCs that feature low calculated singlet‐triplet gaps (ΔE_ST=19.9 kcal mol^?1; B3LYP/def2‐TZVP) and exhibit reactivity profiles expected from triplet carbenes, are described. The electrophilic properties of the CArAmCs were quantified by analyzing their respective selenium adducts, which exhibited the largest downfield ⁷⁷Se NMR chemical shifts (up to 1645 ppm) measured for any NHC derivative known to date, as well as their Ir carbonyl complexes, from which large Tolman electronic parameter (TEP) values (up to 2064 cm^?1) were ascertained. The CArAmCs were found to engage in reactions that are typically observed with triplet carbenes, including C?H insertions, [2+1] cycloadditions with alkenes as well as alkynes, and spontaneous oxidation upon exposure to oxygen.     

Formation,Structural Characterization,and Calculated NMR Chemical Shifts of Selenium‐Nitrogen Compounds from SeCl4 and ArNHLi (Ar = supermesityl,mesityl)

Supermesityl selenium diimide [Se{N(C₆H₂^tBu₃‐2, 4, 6)}₂; Se{N(mes*)}₂] can be prepared in a good yield from the reaction of SeCl₄ and (mes*)NHLi. The molecule adopts an unprecedented anti, anti‐conformation, as deduced by DFT calculations at PBE0/TZVP level of theory and supported by ⁷⁷Se NMR spectroscopy and a crystal structure determination. An analogous reaction involving (C₆H₂Me₃‐2, 4, 6)NHLi [(mes)NHLi] unexpectedly lead to the reduction of selenium and afforded the selenium diamide Se{NH(mes)}₂ that was characterized by X‐ray crystallography and ⁷⁷Se NMR spectroscopy. The Se‐N bonds of 1.847(3) and 1.852(3) Å show normal single bond lengths. The <NSeN bond angle of 109.9(1)° also indicates a tetrahedral AX₂E₂ bonding arrangement around selenium. Two N‐H···N hydrogen bonds link the Se{NH(mes)}₂ molecule with two discrete (mes)NH₂ molecules. In the solid state selenium diamide adopts the anti‐conformation, whereas in solution the presence of both syn‐ and anti‐isomers could be observed. PBE0/TZVP calculations of the shielding tensors of 28 different types of selenium‐containing molecules, for which the ⁷⁷Se chemical shifts are unambiguously known, were carried out to assist the spectral assignment of Se{N(mes*)}₂ and Se{NH(mes)}₂.     

A computational mechanistic study of the deamination reaction of melamine

A detailed computational study of the deamination reaction of melamine by OH^–, n H₂O/OH^–, n H₂O (where n = 1, 2, 3), and protonated melamine with H₂O, has been carried out using density functional theory and ab initio calculations. All structures were optimized at M06/6‐31G(d) level of theory, as well as with the B3LYP functional with each of the basis sets: 6‐31G(d), 6‐31 + G(d), 6‐31G(2df,p), and 6‐311++G(3df,3pd). B3LYP, M06, and ω B97XD calculations with 6‐31 + G(d,p) have also been performed. All structures were optimized at B3LYP/6‐31 + G(d,p) level of theory for deamination simulations in an aqueous medium, using both the polarizable continuum solvation model and the solvation model based on solute electron density. Composite method calculations have been conducted at G4MP2 and CBS‐QB3. Fifteen different mechanistic pathways were explored. Most pathways consisted of two key steps: formation of a tetrahedral intermediate and in the final step, an intermediate that dissociates to products via a 1,3‐proton shift. The lowest overall activation energy, 111 kJ mol^?1 at G4MP2, was obtained for the deamination of melamine with 3H₂O/OH^?.     

Proton affinities of ketones, vicinal diketones and α-keto esters: a computational study

The proton affinities of seven different ketones, vicinal diketones, and α-keto esters (acetophenone, 2,2,2-trifluoroacetophenone, 2,3-butanedione, 1-phenyl-1,2-propanedione, methyl pyruvate, ethyl benzoylformate, and ketopantolactone) have been evaluated theoretically using the conventional ab initio HF and several post-HF methods (MP2, MP4, CCSD), density functional methods with the B3LYP hybrid functional, as well as some ab initio model chemistries [CBS-4M, G2(MP2), and G3(MP2)//B3LYP]. The chemical compounds studied are frequently used substrates in the asymmetric hydrogenation over chirally modified platinum catalysts where the protonation properties of the chiral modifier and the substrates are of great interest. In most cases, the proton affinities (PAs) evaluated with the CCSD/6-311+G(d,p)//B3LYP/TZVP and G2(MP2) methods are in good agreement with the existing experimental ones. However, the previously reported PA of 2,3-butanedione seems to be too high by 10-15 kJ mol⁻¹. The B3LYP/TZVP//B3LYP/TZVP and MP2/6-311+G(d,p)//B3LYP/TZVP model chemistries predict proton affinities that are systematically higher and lower than the experimental PAs, respectively. If proton affinities are evaluated as the average of the PAs calculated with these two theoretical methods a very good agreement with the experimental results is obtained. The mean absolute deviation (MAD) from experiment of this combination method for the PAs of 13 test molecules is 4.0 kJ mol⁻¹. For 9 molecules composed only of first-row atoms the MAD is 2.5 kJ mol⁻¹. The B3LYP/TZVP//B3LYP/TZVP and MP2/6-311+G(d,p)//B3LYP/TZVP methods provide significant savings in computational time and disk space compared to the CCSD/6-311+G(d,p)//B3LYP/TZVP and G2(MP2) models. Therefore, it is suggested that if no experimental or highly accurate theoretical data is available (due to computational cost), the proton affinities of similar compounds as investigated in this paper, can be evaluated with the combination method. For the studied molecules, this method gives the following PAs (in kJ mol⁻¹): 788 (2,3-butanedione, exptl 802); 798 (2,2,2-trifluoroacetophenone, exptl 799); 811 (ketopantolactone); 813 (methyl pyruvate); 825 (1-phenyl-1,2-propanedione); 862 (acetophenone, exptl 861); 865 (ethyl benzoylformate).     

Three‐dimensional networks containing rectangular Sr4 and Ba4 units: Synthesis,structure, bonding,and potential application for Ne gas separation

New porous three‐dimensional metal‐organic frameworks are synthesized that contain infinite chains of Sr_n and Ba_n rectangles. Their structures are elucidated by means of spectroscopic techniques such as nuclear magnetic resonance and Fourier transform infrared, and the respective crystal structures are determined. The electronic structure of basic units of the crystals are computed using density functional theory at the B3LYP/6‐31G(d,p)/def2‐TZVP level, and the bonding and reactivity are analyzed using natural bond orbital analysis, the quantum theory of atoms in molecules, and conceptual density functional theory. The possibilities of noble gas (Ng) storage inside the crystal structures are explored through modeling a Ng atom inside the frozen geometry of the crystal. It was found that a neon atom can fit into a cavity in the Sr and Ba crystal structures whereas other Ngs (He, Ar, Kr) exhibit repulsive interactions with the crystal structure. Ab initio molecular dynamics simulations for up to 500 fs at 77 and 298 K suggest that the structures incorporating a neon atom are kinetically stable. © 2015 Wiley Periodicals, Inc.     

Kinetic Study and NBO Analysis of the Dehydrogenation Mechanism of Five‐membered Ring Heterocyclic 2,5‐Dihydro‐[furan,thiophene, selenophene

The theoretical study of the dehydrogenation of 2,5‐dihydro‐[furan ( 1 ), thiophene ( 2 ), and selenophene ( 3 )] was carried out using ab initio molecular orbital (MO) and density functional theory (DFT) methods at the B3LYP/6‐311G**//B3LYP/6‐311G** and MP2/6‐311G**//B3LYP/6‐311G** levels of theory. Among the used methods in this study, the obtained results show that B3LYP/6‐311G** method is in good agreement with the available experimental values. Based on the optimized ground state geometries using B3LYP/6‐311G** method, the natural bond orbital (NBO) analysis of donor‐acceptor (bond‐antibond) interactions revealed that the stabilization energies associated with the electronic delocalization from non‐bonding lone‐pair orbitals [LP(e)_X3] to δ*_{C(1)  H(2)} antibonding orbital, decrease from compounds 1 to 3 . The LP(e)_X3→δ*_{C(1)  H(2)} resonance energies for compounds 1 – 3 are 23.37, 16.05 and 12.46 kJ/mol, respectively. Also, the LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the decrease of occupancies of LP(e)_X3 non‐bonding orbitals in ring of compounds 1 – 3 ( 3 > 2 > 1 ). The electronic delocalization from LP(e)_X3 non‐bonding orbitals to δ*_{C(1)  H(2)} antibonding orbital increases the ground state structure stability, Therefore, the decrease of LP(e)_X3→δ*_{C(1)  H(2)} delocalizations could fairly explain the kinetic of the dehydrogenation reactions of compounds 1 – 3 (k ₁ >k ₂ >k ₃ ). Also, the donor‐acceptor interactions, as obtained from NBO analysis, revealed that the (_C(4)C(7)→δ*_{C(1)  H(2)} resonance energies decrease from compounds 1 to 3 . Further, the results showed that the energy gaps between (_C(4)C(7) bonding and δ*_{C(1)  H(2)} antibonding orbitals decrease from compounds 1 to 3 . The results suggest also that in compounds 1 – 3 , the hydrogen eliminations are controlled by LP(e)→δ* resonance energies. Analysis of bond order, natural bond orbital charges, bond indexes, synchronicity parameters, and IRC calculations indicate that these reactions are occurring through a concerted and synchronous six‐membered cyclic transition state type of mechanism.     

Quantum chemical study of the autoxidation of ascorbate

Reactions involved in the autoxidation of ascorbate have been investigated with quantum chemical first‐principles and ab initio methods. Reaction energies and Gibbs energies of the reactions were calculated at the density functional theory level applying the gradient‐corrected BP86 and the hybrid B3LYP functionals together with def2‐TZVP basis sets. Results of single‐point CC2, CCSD, and CCSD(T) calculations were used for calibration of the density functional theory data and show excellent agreement with the B3LYP values. Based on the Gibbs energy ascorbic acid AscH₂ is found to be the energetically lowest species in aqueous solution, whereas the monoanion ascorbate AscH is the most abundant one near pH = 7. Asc was found to be the preferred reducing agent for autoxidation and oxidation processes. The results also support a metal‐catalyzed synthesis of the reactive oxygen species H₂O₂ according to a redox cycling mechanism proposed in literature. © 2016 Wiley Periodicals, Inc.     

MPI/OpenMP hybrid parallel algorithm for resolution of identity second‐order Møller–Plesset perturbation calculation of analytical energy gradient for massively parallel multicore supercomputers

A massively parallel algorithm of the analytical energy gradient calculations based the resolution of identity Møller–Plesset perturbation (RI‐MP2) method from the restricted Hartree–Fock reference is presented for geometry optimization calculations and one‐electron property calculations of large molecules. This algorithm is designed for massively parallel computation on multicore supercomputers applying the Message Passing Interface (MPI) and Open Multi‐Processing (OpenMP) hybrid parallel programming model. In this algorithm, the two‐dimensional hierarchical MP2 parallelization scheme is applied using a huge number of MPI processes (more than 1000 MPI processes) for acceleration of the computationally demanding O (N ⁵) step such as calculations of occupied–occupied and virtual–virtual blocks of MP2 one‐particle density matrix and MP2 two‐particle density matrices. The new parallel algorithm performance is assessed using test calculations of several large molecules such as buckycatcher C₆₀@C₆₀H₂₈ (144 atoms, 1820 atomic orbitals (AOs) for def2‐SVP basis set, and 3888 AOs for def2‐TZVP), nanographene dimer (C₉₆H₂₄)₂ (240 atoms, 2928 AOs for def2‐SVP, and 6432 AOs for cc‐pVTZ), and trp‐cage protein 1L2Y (304 atoms and 2906 AOs for def2‐SVP) using up to 32,768 nodes and 262,144 central processing unit (CPU) cores of the K computer. The results of geometry optimization calculations of trp‐cage protein 1L2Y at the RI‐MP2/def2‐SVP level using the 3072 nodes and 24,576 cores of the K computer are presented and discussed to assess the efficiency of the proposed algorithm. © 2017 Wiley Periodicals, Inc.     

Highly efficient implementation of pseudospectral time‐dependent density‐functional theory for the calculation of excitation energies of large molecules

We have developed and implemented pseudospectral time‐dependent density‐functional theory (TDDFT) in the quantum mechanics package Jaguar to calculate restricted singlet and restricted triplet, as well as unrestricted excitation energies with either full linear response (FLR) or the Tamm–Dancoff approximation (TDA) with the pseudospectral length scales, pseudospectral atomic corrections, and pseudospectral multigrid strategy included in the implementations to improve the chemical accuracy and to speed the pseudospectral calculations. The calculations based on pseudospectral time‐dependent density‐functional theory with full linear response (PS‐FLR‐TDDFT) and within the Tamm–Dancoff approximation (PS‐TDA‐TDDFT) for G2 set molecules using B3LYP/6‐31G*^* show mean and maximum absolute deviations of 0.0015 eV and 0.0081 eV, 0.0007 eV and 0.0064 eV, 0.0004 eV and 0.0022 eV for restricted singlet excitation energies, restricted triplet excitation energies, and unrestricted excitation energies, respectively; compared with the results calculated from the conventional spectral method. The application of PS‐FLR‐TDDFT to OLED molecules and organic dyes, as well as the comparisons for results calculated from PS‐FLR‐TDDFT and best estimations demonstrate that the accuracy of both PS‐FLR‐TDDFT and PS‐TDA‐TDDFT. Calculations for a set of medium‐sized molecules, including C_n fullerenes and nanotubes, using the B3LYP functional and 6‐31G^** basis set show PS‐TDA‐TDDFT provides 19‐ to 34‐fold speedups for C_n fullerenes with 450–1470 basis functions, 11‐ to 32‐fold speedups for nanotubes with 660–3180 basis functions, and 9‐ to 16‐fold speedups for organic molecules with 540–1340 basis functions compared to fully analytic calculations without sacrificing chemical accuracy. The calculations on a set of larger molecules, including the antibiotic drug Ramoplanin, the 46‐residue crambin protein, fullerenes up to C₅₄₀ and nanotubes up to 14×(6,6), using the B3LYP functional and 6‐31G^** basis set with up to 8100 basis functions show that PS‐FLR‐TDDFT CPU time scales as N^2.05 with the number of basis functions. © 2016 Wiley Periodicals, Inc.     

Transition structures and reaction barriers in the styrene–acrylonitrile copolymerization system according to quantum mechanical calculations

The geometries and electronic properties of substrates, transition structures (TS), and product radicals in modeled elementary propagation reactions were studied for the styrene–acrylonitrile monomer system by use of quantum‐mechanical calculations: (DFT/B3‐LYP/6–31G(d), ROMP2/6–311+G(3df,2p)//DFT/B3‐LYP/6–31G(d), and DFT/B3‐LYP/6–311+G(3df,2p)//DFT/B3‐LYP/6–31G(d)) and for some parameters, the high‐level composite method G3 (Gaussian‐3, G3/MP2). Activation enthalpies (ΔH^act) and reaction enthalpies (ΔH_r) for modeled propagation reactions at 298.15 K were evaluated. The enthalpy of activation energy (ΔH^act, kJ/mol) for the investigated elementary reactions rises for the B3‐LYP calculation in the following order: (CH₃A?+S) < (CH₃A?+A) < (CH₃S?+A) < (CH₃S?+S). For three propagation reactions, (CH₃A?+A), (CH₃A?+S), and (CH₃S?+A), correlation between reaction enthalpy and enthalpy of activation suggests weak or negligible polar effects reflecting the Evans–Polanyi relation. However, from the electron affinities and ionization energies values data, it is not excluded that at least for [CH₃A?+S[b]] and [CH₃S?+A[b]] reactions, nucleophilic and electrophilic polar effects, respectively, can also be expected. The dependencies between TS geometries, electronic parameters, and enthalpic effects suggest the presence of a steric factor in all TS, including its exceptionally high contribution to the activation enthalpy for the CH₃S?+S addition. © 2005 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 43: 1827–1844, 2005