Poster Session and Mixer 1

Anthropogenic carbon dioxide (CO₂) emissions are a major contributor to rising global temperatures. The adsorption of CO₂ inside Metal-organic frameworks (MOFs), a type of porous material, is a promising way to reduce atmospheric CO₂ levels. Here, we study two MOFs; LMOF-201 and LMOF-202. Previous studies on both Zn-LMOF-202 and Zn-LMOF-201 reveal that both are isostructural, but Zn-LMOF-202 is rigid, whereas Zn-LMOF-201 is flexible. The change in MOFs’ properties by manipulation of their metal cations, organic linkers, and functional groups maintaining the structure topology, makes them highly suitable for CO₂ adsorption. In this work, we propose a novel methodology to enhance the adsorption of CO₂ in MOFs by post-synthetic metal exchange employing Grand Canonical Monte Carlo (GCMC) simulations. Using this computational method, we show that the CO₂ adsorption capacity and selectivity can be magnified by a factor of about 1.5 by changing the metal ion from Zn to In in M-LMOF-202 at 1 bar and 298K. Furthermore, in past, it was found that slight modifications in the ligand part of the LMOF-202 framework by incorporating one oxygen atom into the structure, resulted in flexible LMOF-201. Due to this flexibility, the CO₂ adsorption amount doubled at saturation compared to that of LMOF-202 at 195K. We introduce an approach combining Reactive force field (ReaxFF) and Molecular Dynamics (MD) simulations to capture the structural flexibility of LMOF-201 in presence of CO₂ adsorption. We reproduce the experimental adsorption isotherms of CO₂ in LMOF-201 and observe the existence of two different structures at low and high CO₂ loading respectively. The results of this work show that both LMOF-201 and LMOF-202 have the requisite properties to merit further consideration as a carbon capture adsorbent

Phosphorescent metal complexes continue to play a large role in the design and development of luminescent materials, with a wide range of applications including sensing and display technologies. This is in part due to their long-lived luminescent lifetimes, as well as their ability to harvest both singlet and triplet excitations, leading to theoretical quantum efficiencies of 100%. These factors continue to drive research into improving their photophysical properties. 

We have used DFT methods to explore and benchmark a plethora of luminescent iridium and ruthenium metal complexes, utilizing a variety of alterations in order to modify and enhance their photophysical properties. The character of the frontier orbitals of the complexes, as well as the transitions from TDDFT and socTDDFT calculations have been benchmarked against model complexes, Ir(ppy)₃ and Ru(bpy)₃, in order to determine general rules for modifying and improving the photophysical properties of luminescent metal complexes.

Recently, several groups have investigated ring expansion reactions (RER) of N-heterocyclic carbenes (NHCs) with element hydrides, both experimentally^1-2and theoretically.^3-4Ring expansion involves insertion of the element into the C–N bond of the NHC with formation of an expanded six-membered ring. By investigating the energetics of reaction pathways,⁵we have explored whether RER can be expected for a variety of heteronuclear NHCs (shown below) that are produced by substitution of one nitrogen atom by carbon (CN, cAAC), phosphorus (PN), oxygen (ON) or sulphur (SN). The insertion pathway involved reaction with silane (SiH₄), which readily participates in RER with NHC (NN). We also explored the preference for silane insertion into the nitrogen-carbon bond (N–C) or element-carbon bond (E−C).  

The final products from all of the modelled species are thermodynamically favourable, however, barriers (kinetics) determine the possibility of RER being observed. Our calculations indicate that CN and PN analogues allow facile hydride transfer from the silicon hydride to the carbene carbon, but that subsequent RER is kinetically unfavorable due to large barriers. For both ON and SN, ring expansion is predicted to be experimentally feasible. 

References 

[1] (a) D. Schmidt, J. H. J. Berthel, S. Pietsch, U. Radius, Angew. Chem. Int. Ed. 2012, 51, 8881; (b) H. Schneider, A. Hock, R. Bertermann, U. Radius, Chem. Eur. J. 2017, 23, 12387; (c) D. Franz, S. Inoue, Chem. Asian J. 2014,9, 2083.

[2] L. García, K. H. M. Al Furaiji, D. J. D. Wilson, J. L. Dutton, M. S. Hill, M. F. Mahon, Dalton Trans. 2017, 46, 12015.

[3] Iversen, K. J.; Wilson, D. J. D.; Dutton, J. L., Dalton Trans. 2013,42, 11035.

[4] Al Furaiji, K. H. M.; Iversen, K. J.; Dutton, J. L.; Wilson, D. J. D.  Chem. Asian J., 2018, 13, 3745.

There is an absence of a simple procedure that can produce, from a wavefunction, bond indices between well-defined ``atomic'' entities. Here we further develop and evaluate the Roby-Gould bond index method (RGBI) [Gould et al., Theor. Chem. Acc., 2008, 119, 275] which is based on atomic projection operators representing atoms. 

We report for the first time bond indices obtained using the occupied pre-natural atomic orbitals (NAOs) of natural bond orbital (NBO) theory, and compare these to those previously obtained using the occupied atomic natural orbitals (ANOs) for a dataset of about 400 molecules comprising first-row atoms, and which include a variety of chemical bonds. While the separate covalent and ionic indices from each method are widely different, remarkably, the total bond indices are essentially the same except for molecules which are usually usually termed ``hypervalent''.

We also describe and exhibit a new bond dial diagram to visually display the information from the RGBI method. The dial diagram easily shows when ``back bonding'' occurs.

In molecular spintronics devices based on dipolar nanomagnets, unwanted environmental perturbations easily alter the spin state, corrupting the quantum information. Alternatively, toroidal moments, τ = g μ_B ∑_q r_q x S_q, only interact with the curls of external magnetic fields [1], so toroidal states ought to be less affected than dipolar states by homogeneous magnetic fields or nearby nanomagnets, thus allowing for closer packing in technological devices [2]. Building on previous work [3,4], we discuss how the populations of clockwise and anticlockwise toroidal states would be split if a spin current passed through a spin-frustrated triangular nanomagnet, and discuss why this effect could be monitored by measuring the accompanying change in the spin current’s polarisation [5]. This phenomenon has been previously predicted in strong [3] and weak [4] spin-orbit coupling regimes, and now in the zero spin-orbit coupling regime [5]. Aside from molecular spintronics, our work is also of fundamental importance to the field of molecular magnetism, as we show that spin-frustration alone can lead to a ground manifold with four distinct, degenerate toroidal states.

Figure: Spintronics device based on a triangular nanomagnet with isosceles spin-coupling. Electrons sequentially tunnel from the up-polarised source lead, to the triangle, then to the unpolarised drain lead. The electrons' spins may be switched by exchange coupling with the triangle’s spins, also inducing a net toroidal magnetisation on the triangle.

References
[1] N. A. Spaldin, M. Fiebig, M. Mostovoy, J. Phys.: Condens. Matter, 2008, 20, 434203.
[2] A. Soncini, L. F. Chibotaru, Phys. Rev. B, 2008, 77, 220406(R).
[3] A. Soncini, L. F. Chibotaru, Phys. Rev. B, 2010, 81, 132403.
[4] J. M. Crabtree, A. Soncini, Phys. Rev. B, 2018, 98, 094417.
[5] S. V. Rao, J. M. Ashtree, A. Soncini, 2019, ‘Analytical Prediction of Toroidal States in an Isosceles Spin Triangle without Spin-Orbit Coupling: Applications in a Molecular Spintronics Device’, submitted.

Synopsis: Recent combined theoretical and experimental photoelectron spectroscopic study of biologically significant pyridine derivatives, nicotine, nicotinic acid and nicotinamide, provides insights to intramolecular bonding effects, revealed through rotational conformation. Core Electron Binding Energies (CEBE), Outer Valence Green’s Function (OVGF) and Nuclear Magnetic Resonance (NMR) backed by experimental synchrotron based X-ray studies explore details of symmetry and conformation.  

The pharmacological activity of many organic molecules can be understood through their conformational properties. In order to better understand the structure-property relationship of bio-active species, it is important to monitor changes to electronic structure through subtle structural differences. We provide highlights from our recently submitted paper [1] which reports on the complete electronic spectra of nicotine, nicotinic acid and nicotinamide. Combining theoretical spectra with highly accurate synchrotron sourced X-ray photoelectron Spectroscopy (XPS), we continue to monitor the impact of flexible bond angles on core level energies, expanding on the insights into rotational conformation as a core event gained from our recent Nuclear Magnetic Resonance (NMR) study [2]. While NMR is sensitive to chemical environment, particularly to changes in Hydrogen bonding due to rotational conformation, XPS results found there to be a negligible impact on the core electron structures. The rotation of functional groups was observed to produce a greater impact on valence electron structures, confirmed by OVGF calculations. By dissecting the sigma versus pi electron character of these species on a theoretical level and compare to real-world measurements we can continue to make advancements towards high throughput drug development.  Measurements were obtained at the Gas Phase Photoemission beamline at Elettra-Sincrotrone Trieste, Italy

References [1] Sa’adeh H et al submitted (2019). [2] Backler F et al submitted (2019).

One of the main challenges in the production of all solid state batteries is to fabricate new electrolytes with high ionic conductivities; comparable to traditional liquid electrolytes. Li₇P₃S₁₁ and Li₃PS₄ electrolytes are examples of solid electrolytes with high ionic conductivities. It has been experimentally shown that Ca-doping can improve the ionic conductivity of Li₇P₃S₁₁. However, studying the mechanism of the diffusivity of the pure and Ca-doped samples at the atomic level is still a challenge due to the relatively low ionic conductivity of solid electrolytes and due to the limitations of numerical methods. To study the conductivity and diffusivity of lithium ions in Li₇P₃S₁₁ at the atomic level, we used ab initio molecular dynamics (AIMD) simulations at different temperatures.

In contrast to Li₇P₃S₁₁ are not studies of the effect of a Ca-dopant on the diffusion mechanism in Li₃PS₄. Using AIMD simulations we studied the ionic conductivity of pure Li₃PS₄ and compared the results with the literature. Also, we studied the effect of the dopant on the conductivity of the material and estimated the ionic conductivity of Ca-doped Li₃PS₄ at room temperature.    

The promise of DNA-based catalysts is an exciting one: cheap, largely non-toxic, and easily manipulable, they present as strong competitors to traditional catalysts. One such system, the guanine quadruplex/hemin DNAzyme, catalyses the peroxidation of various substrates and has been the subject of extensive optimisation attempts. Between the agnosticism of catalytic enhancement and the numerous competing steric and energetic factors in the G4/hemin DNAzyme, the catalytic behaviour may have any number of causes. Though the role of the quadruplex is uncertain, recent work¹ has proposed a mechanism in which a necessary, but not sufficient, condition for the peroxidation to occur is the presence of a proximal aryl nitrogen in an overhanging substituent at the 5’ end of the quadruplex. The site functions analogously to histidine in horseradish peroxidase, facilitating a rate-determining proton transfer step from a “traditional” hydrogen-bonded O-H- - -N to the ion pair O^-- - -H-N⁺. Here we show through DFT studies on a simplified system that directed long-range electrostatics may enhance the rate of this proton transfer process. By applying a series of small electric fields along the proton transfer axis, we see significant variation in the topology of reaction paths. Until now, the quadruplex has been treated entirely as a steric contributor, holding the substrates in appropriate arrangements for the enhanced peroxidation. Our work, by contrast, points to the field generated by the quadruplex—namely the cationic backbone, a proximal localisation of positive charge—as a driving factor in the peroxidation enhancement. This aligns with recent shifts towards an understanding of enzymatic catalysis as the provision of a facilitatory preorganised electrostatic environment. By extending our understanding of the role of the quadruplex in the G4/hemin peroxidase mimic to consider electrostatics, we believe that this work may open a new line of inquiry within quadruplex-based DNAzyme chemistry.

The properties of many materials and enzymes/catalysts are based on those of the central metal ions – and these are in turn related to the coordination environment provided by the ligands. To tune these properties, we therefore need to better understand the parameters which affect the size of the ligand field splitting (Δ_o). Spin crossover (SCO) active complexes are perfect for reporting on the fine-tuning of the metal ion environment. 

We recently reported a method to predict the switching temperature T_1/2 of SCO for two different families of iron(II) complexes in solution using the ¹⁵N chemical shift of the coordinating nitrogen (Fig. 1).^[1] In order to more clearly understand how the interaction between the metal ion and its coordination sphere occurs, we have since performed a range of theoretical studies on these families of complexes, aiming to predict the effect of ligand substituent modifications on the ligand field experienced. The ultimate aim is to enable prediction of spin state in solution^[1-2]/solid state^[3] in advance of synthesis. In this presentation our recent theoretical developments and findings will be described.

Fig. 1. Correlation of observed T_1/2 for SCO-active complex with calculated ligand ¹⁵N_A NMR signal for: (red, R²=0.99) five Fe^II(L^azine)₂(NCBH₃)₂ complexes in CDCl₃; and (blue, R²=0.89) sixteen Fe^II(bpp^X,Y)₂(Z)₂ complexes in (CD₃)₂CO (Z = BF₄ for all but one case where it is PF₆).

References:

[1]     S. Rodriguez-Jimenez, M. Yang, I. Stewart, A. L. Garden, S. Brooker, J. Am. Chem. Soc. 2017, 139, 18392-18396.

[2]     L. J. Kershaw Cook, R. Kulmaczewski, R. Mohammed, S. Dudley, S. A. Barrett, M. A. Little, R. J. Deeth, M. A. Halcrow, Angew. Chem. Int. Ed. 2016, 55, 4327-4331.

[3]     K. Nakano, N. Suemura, K. Yoneda, S. Kawata, S. Kaizaki, Dalton Trans. 2005, 740-743

The microscopic understanding of the formation process of the solid electrolyte interphase (SEI) film is an important challenge to design the safe lithium-ion battery (LIB). Attractively, the highly salt-concentrated (HC) electrolyte based on trimethyl-phosphate (TMP) as a unique solvent exhibited a self-extinguishing property in addition to its excellent charge-discharge performance. However, the microscopic mechanism of its SEI layer formation still remains an open question. To investigate such SEI film formation, we used Red Moon (RM) methodology which is the atomistic reaction simulation method recently applied successfully to several secondary battery systems. In the present study, the experimental observations were successfully reproduced where the SEI layers were formed in the “bottom-up” manner resulting in a thinner and denser SEI layer mainly produced through the salt reduction in HC electrolyte. It was revealed that a large amount of salt anions is localized on the SEI surface in HC electrolyte, enhancing the network formation of a dense inorganic layer with SEI salt-derived species. In addition, it was shown that the size of TMP molecule prevents itself from entering in SEI layer, leading to the formation of a pure dense inorganic SEI layer, which should considerably improve the stability of SEI layer and would bring about a long lifetime of advanced safe LIB.

Metal oxide and oxynitride photocatalysts are commonly of a d0 or d10 configuration such as TiO₂, TaON or ZnO and (GaN)_1-x(ZnO)x are studied extensively for solar water splitting applications.[1] In simulating these materials there are main steps of the photocatalytic process to consider: (i) light absorption to generate photogenerated charge carriers; (ii) separation and transfer of charge carriers; and (iii) utilization of charge carriers during surface catalytic reactions.[2]

Computational studies on light active devices have provided insight into band engineering with dopants, surface structure, stability, defects recombination and adsorption of catalytic species.[3] However, in order to accurately simulate such photoactive materials, hybrid and/or range-separated exchange correlation functionals (e.g. HSE06) or GW method are typically required to reproduce experimental bandgaps and intrinsic defects levels. Unfortunately, such methods incur a prohibitive computational cost, this cost often puts severe constraints on the system size that can be modelled.[4] As such the Hubbard-U correction is often applied to LDA and GGA functionals (e.g. PBE, PW91, PBEsol etc.) to recover some degree of accuracy with regards to mitigating the self-interaction error and electron localization.[4]

Herein, we detail the influence tuning a multi-site Hubbard-U correction to provide a better bonding centered view of optical properties, reaction energy, defect formation and migration. We highlight the strengths and pitfalls this method applied to screening and providing quantitative insight on d0 and d10 metal semiconductors for solar water splitting

References:

[1] Cui, J.; Li, C.; Zhang, F., ChemSusChem 2019, 12 (9), 1872-1888.

[2] Y. Ma, X. Wang, Y. Jia, X. Chen, H. Han, C. Li, Chem. Rev. 114 (2014) 9987.

[3] Bai, S.; Zhang, N.; Gao, C.; Xiong, Y., Nano Ener., 2018, 53, 296-336.

[4] Morales-García, Á.; Valero, R.; Illas, F., J. Phys. Chem. C., 2017, 121 (34), 18862-18866.

In the absence of suitable chiral additives, Nuclear Magnetic Resonance (NMR) spectroscopy is blind to chirality due to the space-parity of the shielding and spin-spin coupling tensors. Recently, a theory of chiral discrimination for diamagnetic systems has shown that the space-odd shielding polarizability tensor, a molecular property which accounts for the appearance of a macroscopic electric polarization in the presence of the NMR magnetic field and a rotating nuclear magnetic dipole moment, has opposite sign for two enantiomers. Based on recent work on the theory of paramagnetic NMR, we present and analyze a complete analytic expression for the generalized shielding polarizability tensor, whose isotropic average is proportional to a chiral macroscopic electric polarization measurable in a pulsed NMR experiment probing molecules with an arbitrarily degenerate ground state, providing working expressions for the explicit accurate ab initio calculation of all contributions to the tensor. We recently predicted that this tensor can be measured at room temperature for chiral paramagnetic molecules with a strong magnetic anisotropy (as featured e.g. in lanthanide complexes). We apply our theory by performing ab initio multiconfigurational calculations of all contributions to the tensor for a set of ten trivalent dysprosium complexes which are characterized by a strongly axial ground Kramers doublet and thermally accessible excited Kramers doublets at room temperature. The results show that contributions from thermally populated excited states, while generally reducing the value of the tensor calculated on the assumption of a thermally isolated ground state, do not hinder room temperature detectability of this property for all studied complexes. Trends on the relative sign of dominant contributions are then discussed on the basis of a crystal field model electrostatic potential splitting a ground spin–orbit multiplet, which provides an insight into the properties of the generalized shielding polarizability tensor for open shell species.

Early theoretical investigations¹ into the tautomerisation of free-base porphyrin were restricted to considering the atomic motions within the plane of the macrocycle. The recent advances in both computing power and the density functional theory treatment of dispersion forces provides the opportunity to revisit this subject in a more comprehensive manner. By devising a sophisticated coordinate system to describe the annular positions of the H-atoms, and explicitly addressing “cross-bonded” structures, we have generated the full potential energy surface for the tautomerisation of free-base porphyrin and identify novel minima and transitions structures of various orders. A new and compact notation derived from consideration of the symmetry perturbation properties of the system is introduced in order to uniquely and systematically describe these stationary points, and doubles as check for the completeness of the set of structures. Of broader relevance, these act as structural prototypes for other porphyrin systems and provide inspiration for synthesis.

References:
1.   Reimers JR, LuÈ TX, Crossley MJ, Hush NS (1995) J Am Chem Soc 117:2855

Double-hybrid density functionals (DHDFs) are nowadays the most accurate and robust functionals in density functional theory (DFT) for ground-state[1,2] and excited-state properties[3,4,5], positioned on the highest rung on the Jacob’s Ladder of DFT approximations. DHDFs made a major step forward including not only occupied orbitals, as previous approaches, but also unoccupied ones to better describe non-local electron-correlation effects. Nevertheless, the lack of a long-range correction scheme makes them unreliable when it comes to long-range interactions, a flaw that they share with every non long-range corrected functionals. For this reason, we recently proposed the first two double-hybrid functionals with correct asymptotic long-range behaviour optimised for excited states named ωB2PLYP and ωB2GPPLYP[6]. Herein, we review their excellent performance and show that they are the most accurate and robust density functional theory methods for electronic excitation energies, as they provide a balanced description of local-valence, Rydberg and charge-transfer states. They are also able to tackle the difficult first two transitions in polycyclic aromatic hydrocarbons and show very promising results in a preliminary study on transition metal compounds, which is exemplified for titanium dioxide clusters. We then conclude with an overview of other strategies to further improve time-dependent double hybrids and the insights that we gained from them[7].
[1] Goerigk L. and Grimme S., Phys. Chem. Chem. Phys.2011,13,6670–6688.
[2] Goerigk L. and Hansen A. and Bauer C. and Ehrlich S. and Najibi A. and Grimme S., Phys. Chem. Chem. Phys.2017,19,32184–32215.
[3] Grimme S. and Neese F., J. Chem. Phys.2007,127,154116.
[4] Goerigk L. and Grimme S, J. Chem. Theory Comput.2011,7,3272–3277.
[5] Schwabe T. and Goerigk L, J. Chem. Theory Comput.2017,13,4307–4323.
[6] Casanova-Páez M. and Dardis M. B. and Goerigk L., J. Chem. Theory Comput.2019, Published online, doi:10.1021/acs.jctc.9b00013.
[7]  Casanova-Páez M. and Goerigk L., manuscript in preparation.

Accurate modelling of solute-solvent interactions is crucial for reliable prediction of the outcomes of condensed phase reactions. In this poster, we present a general approach to systematically improve molecular mechanics explicit solvent simulations through an end-point correction scheme for a simple yet fundamental organic reaction.¹ As part of this effort, we have further carried out an extensive assessment of a range of high-level ab initio composite methods and DFT methods, from the lower to upper rungs of Jacob’s DFT Ladder, against benchmark DLPNO-CCSD(T)/CBS solute-solvent interaction energies of neutral and charged solutes. This poster will highlight several strategies for the development of a systematically improvable and cost-effective solvent model for condensed phase simulations. 

(1) Chen, J.; Shao, Y.; Ho, J. Are Explicit Solvent Models More Accurate than Implicit Solvent Models? A Case Study on the Menschutkin Reaction. J. Phys. Chem. A 2019 123 (26), 5580-5589. DOI: 10.1021/acs.jpca.9b03995

The infrared (IR) spectrum is related to the Fourier transform of the dipole (or dipole-derivative) correlation function, whose quantum version in principle leads to exact vibrational frequencies. Hence, there is then a great deal of effort focus on developing accurate real time quantum dynamics methods. Path integral Liouville dynamics (PILD), a novel imaginary time path integral-based dynamics approach that we have recently developed [2], can reproduce exact results in the harmonic limit for correlation functions (even with nonlinear operators) as well as conserve the equilibrium distribution of quantum canonical ensemble. PILD has been shown to give accurate vibrational spectra for real molecules, e.g. OH, H2O, NH3, and CH4[3]. In this work we study several molecules that are often used as benchmark calculations, including H2O2, CH2O, and H5O2+. By employing the “Middle” scheme [4] that we have developed recently, PILD can use larger time steps without loss of accuracy during the evolution of the real time trajectory. Comparison to exact vibrational frequencies demonstrates that PILD produces a reasonably accurate peak position with a relatively small full width at half maximum.

References
[1] J. Liu et al., J. Chem. Phys. 135, 244503 (2011); M. Shiga et al., Chem. Phys. Lett.451, 175 (2008); A. Witt et al.,J. Chem. Phys. 130, 194510 (2009); S. D. Ivanov et al., J. Chem. Phys.132, 031101 (2010); M. Rossi et al., J. Chem. Phys. 140, 234116 (2014).
[2] J. Liu, J. Chem. Phys.140, 224107 (2014).
[3] J. Liu, Z. Zhang, J. Chem. Phys.144, 034307 (2016).
[4] Z. Zhang et al., J. Chem. Phys.147, 034109 (2017).

The Nazarov cyclisation is the 4π-electron conrotatory cyclisation of a 3-hydroxypentadienyl cation. Asymmetric catalysts are commonly used to induce enantioselectivity in these reactions. BINOL-derived catalysts have gained special popularity for this purpose in recent years.

This study examines asymmetric Nazarov cyclisations mediated by two BINOL-derived catalysts: a BINOL phosphoric acid and an H₈-BINOL phosphorodithioic acid. Despite their similar chemical structures, these two catalysts give very different enantioselectivities in the cyclisation of 1. BINOL-derived phosphoric acid 3 gave 81% ee¹ while H₈-BINOL phosphorodithioic acid 4 gave only 9% ee² This presentation will describe the results of DFT calculations of the catalytic mechanism and chiral induction mechanism of the two BINOL-derived catalysts.

Prevalence of mentholated products for consumption has brought great importance to studies on menthol’s metabolic pathways to ensure safety, design more potent derivatives, and identify therapeutic benefits. This in silico study supplements previous studies by constructing tentative metabolic pathways of (-)-menthol based on metabolites found experimentally in previous work by Yamaguchi, Caldwell & Farmer, Madyastha & Srivatsan and Hiki et al. The reactions involved in the pathways are conjugation to glucuronide & sulfate, oxidation to alcohol, aldehyde & carboxylic acid, and formation of four/five-membered ring. Gas-phase structures, the standard Gibbs energies and SMD solvation energies at B3LYP/6-311++G(d,p) level were obtained for 102 compounds in the pathways. This study provides a more complete picture by filling the gaps within menthol metabolism as previously proposed.

The density-functional tight-binding (DFTB) method is an approximated DFT method with careful approximations. It uses pre-computed parameters either directly computed from DFT or optimized from reference ab initio or DFT calculations, which makes it robust and suitable for treating large systems. In the past decades, several general or specific parameterization sets have been developed. The recently developed DFTB parameterization set for organic and bio-organic systems, 3ob, has been extensively tested and successfully applied to many applications. It has also been extended to cover several metal elements including Mg, K, Ca, Zn, Ni, and Cu. However, those metal parameters were parameterized mainly for the biochemical systems and the performance for other metal-containing systems are not clear. In this poster, we are presenting the use of the previously developed automatized parameterization scheme for metal-containing systems, including metal-organic frameworks (Cd, Al, and Cu), metal cluster (Pt, Pd, and Rh) and metal oxide (Al) surfaces, and lithium-ion battery electrolyte solutions. We believe that the automatized parameterization scheme and the newly developed parameterizations would enhance the availability of employing the DFTB method to more various systems. 

The phototautomerisation of acetaldehyde, CH₃CHO, to vinyl alcohol, CH₂CHOH, occurs in tropospheric conditions. Subsequent reaction of CH₂CHOH with OH radicals produces formic acid, HCOOH; this reaction accounts for 7% of global atmospheric HCOOH. 

The tautomerisation of CH₃CHO to CH₂CHOH occurs on the highly vibrationally exited (‘hot’) electronic ground state of CH₃CHO, S₀. As such, the yield of CH₂CHOH in the atmosphere from this process depends on the energy-dependent intersystem crossing rates returning photoexcited CH₃CHO to S₀, the rate of tautomerisation on S₀, and the rate and magnitude of collisional energy transfer (CET) between hot CH₃CHO/CH₂CHOH and N₂. While there is theoretical data describing the intersystem crossing and tautomerisation rates, no direct experimental or theoretical data exists for the CET. A previous study of this tautomerisation reaction in the atmosphere modelled CET by fitting an exponential-down model with a single, energy independent, parameter, to CH₃CHO photodissociation yields at various pressures and wavelengths; this same model and parameter were used to describe CET for both CH₃CHO and CH₂CHOH with N₂. 

This work seeks to improve upon the model of CET between CH₃CHO/CH₂CHOH and N₂. Is an exponential down model, with a single, energy-independent parameter, appropriate to describe CET in this system? Is it valid to use the same model and/or parameters for both CH₃CHO and CH₂CHOH? To answer these questions, we use classical trajectory simulations to model collisions between hot CH₃CHO/CH₂CHOH and N₂, with conditions as close as possible to those in the atmosphere. We define internal potential energy surfaces (force fields) for each collision partner, and an interaction potential between CH₃CHO/CH₂CHOH and N₂, considering both the Lennard-Jones potential and a modified exponential-6 formulation. We find that the single parameter exponential model is not appropriate in this system, and that the CET is both energy dependent and different for each tautomer. 

Nuclear magnetic resonance (NMR) spectroscopy is one of the most powerful and versatile spectroscopic tools for chemical analysis and structural determination. However, it is often impractical to interpret and assign NMR spectra for complex molecules by hand and computational methods are often introduced. Ab initio NMR calculations are often accurate and have high sensitivity to structural and electronic changes, allowing regioiosmers to be distinguished. However, ab initio NMR has issues with diminished accuracy for some molecules such as fluororganics, which can be attributed to the inability of Gaussian basis functions to describe the electron-nuclear cusp. 

This study involves a novel type of basis set, called the mixed ramp-Gaussian basis set¹ which involve a new kind of primitive function – the ramp, which has an electron-nuclear cusp. In initial tests with low angular momentum basis functions, mixed ramp-Gaussian basis sets have been shown to be as fast as conventional all-Gaussian basis sets² for moderate sized molecules, and to reproduce the electron density at the nucleus far better³. For further testing, we have developed a set of pseudoramps, which model ramp functions as a large linear combination of Gaussians. These pseudoramps can be used to predict the calculation results which can be obtained using newly derived mixed ramp-Gaussian basis sets based on parent all-Gaussian basis sets, without full coding and interfacing of the mixed ramp-Gaussian integral package.

We present details of the new mixed ramp-Gaussian basis sets for elements up to Ar, as well as parameters for the pseudorampification for these elements. We also present initial results of using the pseudorampified basis sets to predict NMR chemical shifts.

References

(1)  – J. Chem. Theory Comput., 2014, 10, 4369.

(2)  – J. Chem. Theory Comput., 2015, 142, 134104.

(3)  – J. Chem. Theory Comput., 2015, 11, 3679.

We describe the first ab initio aspherical X-ray structure refinement for polypeptides and proteins, using a fragmentation approach to break up the protein into residues and solvent, and thereby speed up the quantum-crystallographic Hirshfeld atom refinement (HAR). We find that the geometric and atomic displacement parameters from the new fragHAR method are essentially unchanged from a HAR refinement on the complete unfragmented system when tested on di-, tri- and hexapeptides. The largest changes are for parameters describing hydrogen atoms involved in hydrogen-bond interactions, but we show that these discrepancies can be removed by including the interacting fragments as a single larger fragment in the fragmentation scheme. Significant speedups are observed for the larger systems. With this approach we are able to perform a highly parallelized HAR in reasonable times for large systems. The method is implemented in the TONTO software.

Mechanical ball milling has been used for chitin depolymerization to N-acetylglucosamine (GlcNAc) in which acid requirement have been reduced significantly. The synergy of mechanical activation and acid catalysis afforded higher selectivity of glycosidic bond cleavage over amide bond breakage in lower acid concentrations. Hence, the bioactive GlcNAc monomer was preferentially produced over glucosamine while maintaining lower acid wastes. In this regard, the force dependent mechanochemical activation-deactivation in relaxed and pulled GluNAc dimer undergoing deacetylation and depolymerization reactions have been studied. Relaxed depolymerization and deacetylation reactions have been studied with GlcNAc dimer in a protonated (+1) mixed implicit/explicit water environment using an in-house Modified Gaussian09 at B3LYP/6-311g(d,p) level. Activation Energies (E_A) of Rate Determining Steps (RDS) proved that the two reactions could occur simultaneously. Force Modified Potential Energy Surfaces (FMPES) were then sampled. Mechanical force was introduced explicitly in the rate determining steps of both reactions. Force modifications were done with magnitudes up to 3.0 nN in three unique pulling directions. In general, as applied pulling force increases, the E_A of the RDS of deacetylation increases while that of depolymerization decreases. This result agrees to the selectivity found in the experiment. Energy and structural analyses for the depolymerization showed that activation can be attributed to conformational change of the reactant which leads to a decrease interaction with water. The active site showed a significant change in glycosidic dihedral which leads to e^- donation to the σ^∗ orbital of the glycosidic bond leading to the activation. Consequently, the Bronsted-Løwry basicity of the glycosidic oxygen also increased which would lead to acid catalysis.

The oxidation of aryl-amine substrate to aryl-nitro product catalyzed by the N-oxygenase (CmlI) is the final step of antibiotic chloramphenicol biosynthesis. The binuclear non-heme iron centers of CmlI, activate O₂ molecular oxygen to initiate the reaction through making of bridged Fe-O bond, followed by oxygenation of aryl-amine substrate and hydrogen atom abstraction. The shuttling of electrons from two iron centers to the substrate is the key factor for the entire reactions. This computational study is dedicated to elucidate the mechanism of the catalytic conversion of aryl-amine substrate to the aryl-nitro product and electronic structure of intermediate of the bi-nuclear iron enzyme. The influences of different spin states of iron centers are also studied for the entire schemes.  Density functional theory computations on the structure and mechanism established here show that the initial Proton-Coupled Electron transfer (PCET) steps activate by peroxide intermediate through single electron transfer (SET) reactivity. The spin variation on the reactive iron centers relatively influenced the activation energy of PCET steps. The DFT study with reductionist approach CmlI shows that its electronic and geometric structures are poised to react speedily with the O₂ molecule. Based on the study of the previous computations of peroxy biferric model complexes, UB3LYP functional and the 6-31G* basis set for geometry optimizations and frequency calculations and the 6-311G* basis set for single-point energy calculations were opted with the Gaussian 09 package

References :

1.      Jasniewski, A. J.; Komor, A. J.; Lipscomb, J. D.; Que, Jr, L. J. Am. Chem. Soc. 2017, 139, 10472-10485

2.      Sutherlin, K. D.; Rivard, B. S.; Bottger, L.H.; Liu, L. V.; Rogers, M. S.; Srnec, M.; Park, K.; Yoda, Y.; Kitao, S.; Kobayashi, Y.; Saito, M.; Seto, M.; Hu, M, Zhao, J.; Lipscomb, J.D.; Solomon, E.I. J. Am. Chem.  Soc.  2018, 140, 16495-16513. 

Atom Transfer Radical Polymerisation (ATRP) has revolutionised polymer synthesis; enabling the precise construction of sophisticated macromolecules under mild conditions. In ATRP, a redox active metal mediator (usually Cu) activates a ‘dormant’ organohalide initiator, generating carbon-based radicals that can be harnessed for polymer chain growth. Crucially, this reaction is reversible and so ‘living’ polymerisations can be achieved by carefully balancing this activation/deactivation equilibrium (K_ATRP). While current ATRP methodology can polymerise a wide-array of monomers, activation of less-stabilised alkenes remains problematic. Indeed, for monomers such as vinyl chloride and vinyl acetate, the N-based ligands usually employed in Cu-base d ATRP are not sufficiently activating. In this work, we use high-level computational theory to assess the performance of P-based ligands in Cu-based ATRP. First, we examine how structural features of a diverse set of ligands affect K_ATRP. Next, we establish rational design criteria based on electrostatic arguments and ligand-field theory. Finally, using these design criteria, we propose a range of ‘next-generation’ ATRP ligands that are predicted to have unprecedented activity.

Liquid phase heterogeneous catalytic reactions have gained popularity as an alternative method of forming products which are otherwise not feasible in gas-phase. Stability of products in the liquid phase is extremely important for a high extent of reaction. Our group has recently developed a liquid phase catalytic reaction for formaldehyde synthesis using syn-gas [1]. CO and H₂ react at the surface of Ni-Ru catalyst particles suspended in methanol-water mixtures to produce formaldehyde. Formaldehyde yield is significantly affected by the composition of methanol-water mixture (Fig. 1a) [1]. To understand the effect of liquid phase, we performed classical molecular dynamics simulations. We observed that the strength of hydrophobic and hydrophilic interactions changes on changing methanol-water mixture composition. In pure methanol, solvated formaldehyde (methoxymethanol) is stabilised in an 8-10 membered methanol ring/chain structure (Fig. 1b). However, at low methanol compositions, hydrophobic clustering of methanol around solvated formaldehyde (methanediol and/or methoxymethanol) is observed (Fig. 1c). These clusters stabilise formaldehyde in the liquid phase and hence a higher yield of formaldehyde is observed experimentally (Fig. 1a). At near equimolar compositions, the strong hydrophilic nature of water prevents the formation of ring/chain structures and, also,  hydrophobic clustering is not favoured (Fig. 1d). Consequently a lower yield of formaldehyde is observed at near equimolar compositions. This changing micro-phase structure can potentially explain various other thermodynamic anomalies of formaldehyde-methanol-water mixtures.

Figure: (a) Formaldehyde yield on varying methanol concentration [1], (b) methoxymethanol surrounded by ring/chain structure in pure methanol [1], (c) spatial distribution function at 0.3 methanol mole-fraction (blue iso-surface represents methanol whereas red wireframe represents water), (d) schematic of hydrophobic (blue enclosure) and hydrophilic (red enclosure) molecular arrangement at near equimolar methanol-water mixture compositions.

References: 

1. Bahmanpour,     A. M., Hoadley, A., Mushrif, S. H., and Tanksale, A. ACS     Sustainable Chemistry & Engineering 4, 3970 (2016).

Sodium proton exchanger isoform 1 (NHE1) is a ubiquitously expressed integral transmembrane glycoprotein that controls the electroneutral exchange of a single intracellular proton for one extracellular sodium ion across the plasma membrane in all mammalian cells and thus elevating the intracellular pH [1]. NHE1 protects cells from intracellular acidification, and plays key roles in regulating the cell volume and proliferation [2]. Elevated NHE1 levels were found to trigger metastasis especially in breast cancer. [3] The complete crystal structure of NHE1 hasn’t been resolved so far. Understanding the mechanism of Na⁺/H⁺ exchange across NHE1 is important for the future development of clinically useful NHE1 inhibitors.

In this work, three-dimensional homology models for the inward-facing and outward-facing NHE1 states were built based on the crystal structures of Methanocaldoccocus jannaschii (MjNhaP1). MjNhaP1 is the most similar Na⁺/H⁺ antiporter to NHE1 with 20% sequence identity and 38% similarity. Molecular dynamics (MD) simulations, steered molecular dynamics (SMD) simulations potential of mean force (PMF) calculations and molecular docking studies were performed in order to predict the structure of NHE1, understand the mechanism of Na⁺/H⁺ transport across the membrane and inhibitor binding. Our computational studies have provided detailed mechanistic interpretation to experimental data and serve the basis of future structure-based inhibitor design.

References

1. J. Orlowski, S. Grinstein, J. Biol. Chem., 272, 22373 (1997). 
2. L. Fliegel, Int. J. Biochem., Cell Biol. 37, 33 (2005). 
3. S. R. Amith, L. Fliegel, Cancer Res., 73, 1259 (2013).

N-heterocyclic carbenes (NHCs) are an important and widely used class of organocatalysts. Singlet carbenes of NHCs serve as both ligands for organometallic catalysts as well as catalysts in their own right, more prominently as nucleophilic species in Umpolung chemistry, but also as Brønsted bases in organic transformations. The basicity of these compounds is inevitably linked to their reactivity and is important for their ability to mediate a broad range of complex chemical transformations[1]. However, there have been few systematic studies (experimental or computational) of the basicity of NHCs.

In this poster, we present a comprehensive and systematic benchmarking study, assessing the performance of a range of high-level ab initio methods, density functional theory (DFT) and semi-empirical QM methods. The study covers the 5 main classes of carbenes; imidizoles, triazoles, thiazoles, oxazoles and saturated systems and provides quantitative insight on the structure-basicity relationship of these compounds. Finally, we propose several cost-efficient methods for accurate prediction of gas phase basicity that may be used to help guide the design of better catalysts.

[1] Wang N, Xu J, Lee J, Org. Biomol. Chem., 2018, 16, 8230

The electronic absorption spectra of some small sulfur-containing molecules of atmospheric importance have been simulated using a nuclear ensemble approach with the Newton-X package. The ensemble is based on Wigner sampling of vibrational frequencies calculated at the CCSD(T) level of theory with the aug-cc-pV(T+d)Z basis set. The electronic excited state transition energies and oscillator strengths of each geometry in the ensemble are calculated with the EOM-CCSD, RI-CC2 and ADC(2) methods using correlation consistent basis sets with additional diffuse basis functions, denoted aug-cc-pV(X+d)Z+3. 

We find very good agreement between our calculated spectra and the available experimental spectra of sulfur dioxide (SO₂), sulfur trioxide (SO₃), hydrogen sulfide (H₂S), carbonyl sulfide (OCS) and carbon disulde (CS₂). We show that computational cost of these simulated spectra can be substantively reduced with negligible loss of accuracy by using a combination of results obtained with the aug-cc-pV(D+d)Z+3 and aug-cc-pV(T+d)Z+3 basis sets. 

Sulfuric acid (H₂SO₄) is the dominant form of atmospheric sulfur in the stratosphere and plays an important role in terms of aerosol formation. However, despite its atmospheric significance, the experimental spectrum of H₂SO₄ is not yet known, although there have been multiple attempts to record it. We apply our simulation approach to calculate the electronic absorption spectrum of H₂SO₄, considering the two low-energy conformers that are abundant under atmospheric conditions. Above 6.4 eV, we find that our calculated spectrum for H₂SO₄ is generally in agreement with the experimental upper limits for the absorption cross-section. However, below this energy there is more uncertainty and we suggest that further experimental investigation is needed.  

[Introduction] For treating large systems such as proteins, a lot of fragmentation-based electronic structure methods have been developed. These methods, however, introduce the errors associated with the fragmentation. In addition, especially in proteins, the weak interactions (e.g., dispersion force) usually play important roles to stabilize the higher-order structure. We have developed the divide-and-conquer (DC) method [1] and reported the automatic fragmentation scheme in the DC-SCF calculation [2]. In this study, we extend this scheme to the DC-MP2 electron correlation calculation [3].

[Theory] Each fragment of the DC method consists of the disjoint central region and its neighboring region called the buffer region. In the DC method, the energy error can systematically be decreased by increasing the size of the buffer region. However, the appropriate size of the buffer region depends on the system. In this study, based on the atomic orbital Laplace MP2 method [4] and Schwarz inequality, we derived the upper bound of the electron correlation energy contribution for each atom in the buffer regions. We developed a method to automatically determine the buffer region in the DC-MP2 calculation by establishing energy threshold for this upper bound.

[Numerical assessment] The present method was applied to 100 water molecules. The energy error and the fragment size with respect to the energy threshold is showed in Figure. The energy error decreased and the average fragment size <r> increased systematically as the energy threshold e_thresh decreased. Therefore, it is conformed that the appropriate size of the buffer region can be selected in each fragment based on the DC-MP2 energy.

[1] W. Yang and T.-S. Lee, J. Chem. Phys. 1995, 103, 5674.

[2] M. Kobayashi, T. Fujimori, T. Taketsugu, J. Comput. Chem. 2018, 39, 909.

[3] M. Kobayashi, et al., J. Chem. Phys. 2007, 127, 074103. 

[4] M. Häser, Theor. Chim. Acta 1993, 87, 147.

An optimization of reaction condition is one of the most important but highly costing tasks in experiments to obtain desirable results. To realize the rational optimization, it is necessary to control various kinds of chemical conditions including continuous and discrete variables. Recently, optimization schemes for continuous reaction conditions such as reaction time, temperature, concentration, and scale, have successfully been developed with the advances of flow reactor equipment. However, there are still a few practical rational optimizing examples for discrete reaction conditions such as solvents, reductant, and catalysts. In addition, an optimization in small number of experiments is desired because individual batch reactions are performed by human hands in usual laboratories. In this study, we investigated the optimization of reaction conditions for two different organic reaction systems including discrete conditions with small number of experiments. Machine learning was utilized to analyze relationships between reaction conditions and yields of chemical reactions. In the first reaction system, an optimization of high dimensional reaction conditions including discrete variables was investigated [1]. The discrete conditions were represented in binary vectors for machine learning. The scheme reasonably performed to reduce the experimental attempts. In the second reaction system, a solvent selection scheme was investigated in the reaction conditions because the reaction is highly sensitive to the solvent [2]. The characteristics of solvents were numerically represented in their physical properties. The scheme showed a potential to predict chemical yields for solvents before performing experiments.

[1] M. Fujinami, J. Seino, T. Nukazawa, S. Ishida, T. Iwamoto, and H. Nakai, Chem. Lett., 48, 961 (2019).

[2] M. Fujinami, H. Maekawara, J. Seino, R. Isshiki, J. Yamaguchi, and H. Nakai, in preparation.

Nitroxide mediated polymerization (NMP) confers living characteristics on radical polymerization through reversible deactivation. Despite the advantages of a “living” mechanism, NMP requires elevated temperatures (above 100 °C) for the reaction to occur in a reasonable time frame. An alternative is nitroxide mediated photopolymerisation (NMP²) where a chromophore is added, enabling photocleavage of the alkoxyamine bond from the energy provided by light in the U.V range ¹. However, a good photoiniferter is proving difficult to design. Previous work has shown that the choice of chromophore, its position in the molecule, competitive pathways for cleavage and energy dissociation all need to be considered when developing an NMP² initiator ^{2 3}. In the present work, we use high-level quantum chemistry to explore potential photocleavage mechanisms of a wide array of NMP² initiators with the aim to correlate their structure and reactivity. The influence of potential side reactions is also investigated. 

References

¹ Y. Guillaneuf, D. Bertin, D.Gigmes, D.-L. Versace, J. Lavalée, J.-P. Fouassier. Macromolecules, 2010, 43, 2204-2212

² M. Huix-Rollant, N. Ferré. The Journal of Physical Chemistry A. 2014, 118, 4464-4470

³ S. Bottle, J.-L. Clement, M. Fleige, E. Simpson, Y. Guillaneuf, K. Fairfull-Smith, D. Gigmes, J. Blinco. Royal Society of Chemistry Advances. 2016, 6, 80328-80333

Specific-ion effects (SIEs) induce or influence physicochemical phenomena in a way that is determined by the identity of the ions present, and not merely by charge or concentration. Such effects have been known since the seminal work of Hofmeister and are often categorised according to the well-known Hofmeister series. Examples of SIEs are ubiquitous throughout chemistry and biology, and are traditionally explained in terms of the influence ions have on the structure of water. However, this explanation is unsatisfactory as it is unable to adequately explain and predict frequently-observed series reversals and anomalies. By modelling solvated ion-N-isopropylacrylamide (NIPAM) complexes with GKS-EDA, we show that ion-NIPAM interaction free energies are predominantly independent of the counterion, even in ion-pairs. However, ion-pairing can modulate repulsive ion-NIPAM interactions and thus induce a Hofmeister series reversal.

Non-ionic surfactants containing polyethylene oxide (PEO) head groups are widely used in drug formulations, paints, cosmetics, textiles and detergents. In our research, we are interested in PEO surfactants as excipients in lipid-based drug formulations. Molecular dynamics (MD) simulation is a useful tool for obtaining atomic scale information, which helps to understand the colloidal structure formation of these PEO surfactants. However, many existing force fields do not reproduce the experimental phase behaviour of PEO due to the poor parameterisation of oxy functional groups and vicinal ethylene oxide groups, thus MD simulations with PEO molecules lag behind. The present study was carried out to identify a whether the recently released GROMOS force fields, 2016H66 developed to model the ‘gauche effect’ of PEO and 53A6_DBW developed to model interactions between water and ethylene oxide chains adequately models PEO surfactants. In this work, we performed extensive MD simulations using those two force fields to model the aqueous phase behaviour of the simple non-ionic surfactant, hexaethylene glycol monododecyl ether (C₁₂E₆), and then compared the simulated phase behaviour with experimental observation. From these simulations, we found that 2016H66 force field reproduced the experimental phase behaviour of C₁₂E₆/water systems better than 53A6_DBW. In conclusion, our study showed that spontaneous aggregation of PEO surfactants into different colloidal structures can be successfully modelled with 2016H66 force field.

DNA is able to change its conformation when exposed to different conditions.[1] Infrared (IR) spectroscopy, a technique that studies the interaction of light and bonds and functional groups present in a sample, has been utilised to study the structural changes when DNA is exposed to different conditions.[1] B-DNA has been shown to convert to A-DNA when the hydration level falls below 75%., resulting in a shift  in  v_asymPO₂⁻   from  1240  to  1220  cm⁻¹.[2, 3]  In  addition,  the  v_symPO₂⁻   peak  at  1080 cm⁻¹ becomes more intense after hydration.[2, 3] With the ability to accurately characterise DNA conformation, this opens the possibility of using IR spectroscopy as a tool to study DNA-drug interactions.  To explain the shifts in v(PO₂⁻ ), Fragment Molecular Orbital (FMO) with Frozen Dimer Domains (FMO/FDD) is used.[4]

FMO, a method that fractions large systems into smaller fragments, is a cost efficient and accurate theory, a suitable method to study large biomolecule.[4] FMO/FDD allows for frequency calculations to be performed on the fragments of interest, decreasing computational cost while not compromising on the accuracy of the calculation.[4]

In this study, we utilised the FMO approach to study DNA models, in particular single-stranded models that comprises of 1 and 2 nucleobase pairs. The effect of a varying degree fragmentation on IR spectra was explored and the calculated results were compared with experimental data. In addition, the inclusion of both implicit and explicit solvation models, on the prediction of IR frequencies is also investigated.

[1]      B. R. Wood, 2016, Chem. Soc. Rev., 45, 1980–1998.

[2]     J. Pilet, J. Brahms, 1972, Nature New Biology, 236, 99.

[3]     Z.-J. Tan, S.-J. Chen, 2006, Biochem, J., 90, 1175–1190.

[4]     D. G. Fedorov, Y. Alexeev, K. Kitaura, 2011, J. Phys. Chem. Lett., 2, 282–288.

      In this study, the mechanism of H₂ oxidation and production reactions using homogeneous Ni catalysts with the different R and R’ substituent groups of ligand complexes on the singlet and triplet states were investigated using DFT calculations. The potential energy profiles of four [Ni(P^R₂N^R’₂)₂]²⁺ complexes when (R, R’) substituent groups of  ligands which consist of (H, H), (Me, H), (Me, Me) and (Cy, Me) were compared. The results revealed that the bare active site, the singlet state was calculated to be more stable than the triplet sate. Moreover, we found that the energy between the singlet and triplet states depend on geometry of complex. For calculated potential energy pathway involved the minimum-energy intersystem crossing point (MEICP) between the singlet and triplet states, there are two MECPs (MECP1 and MECP2) have been observed around TS1. The MECP1 geometry is similar to hydride-proton intermediate, and the geometry of MECP2 is H₂ complex. Therefore, analysis of the reaction coordinate of MECP structure showed that the energy gap between the singlet and triplet states significantly depends on distortion of geometry. This knowledge could be useful for ligand design to develop more efficient catalysts.

Azulenequinone/hydroquinone molecules, known as non-alternant hydrocarbon compounds, can achieve promising moletronic applications due to the advantageous tunability of azulene via its conversion to its quinone. Given 1,5- and 1,7-azulenequinones are already synthesized and considered the most stable forms of azulenequinones, we investigate such promising candidates for molecular electronic miniaturization using first principles density functional theory and non-equilibrium Green’s function theory. The current-voltage characteristics of these molecules display a switching behaviour, with a switching ratio of 35, at low bias, in the 1,5-stable hydroquinone over quinone 2,6-azulene dithiolate, thus showing a redox molecular switch function. To understand the reason for current switching, we analyse the molecular orbitals obtained from first principles calculations and compare them with diagrammatic quantum interference calculations.  Exploring multiple theoretical DQI models [3,4] allowed us to examine whether destructive quantum interference (DQI) plays a role or not [1,2] in our electronic transport study. The different theoretical models yielded contradicting results on the existence of DQI in 1,5-azulenequinone. Our work provides a theoretical foundation from a DQI perspective which predicts electron-transport properties for organic redox switching components in nano-electronics circuits. 

[1] Markussen, T., R. Stadler, and K.S. Thygesen, The Relation between Structure and Quantum Interference in Single Molecule Junctions. Nano Letters, 2010. 10(10): p. 4260-4265.

[2] Markussen, T., R. Stadler, and K.S. Thygesen, Graphical prediction of quantum interference-induced transmission nodes in functionalized organic molecules. Physical Chemistry Chemical Physics, 2011. 13(32): p. 14311-14317. 

[3] Sỳkora, R.; Novotnỳ, T. Graph-theoretical evaluation of the inelastic propensity rules

for molecules with destructive quantum interference, J. Chem. Phys. 2017, 146, 174114, 12.

[4] Tsuji Yuta, Ernesto Estrada, Ramis Movassagh, and Roald Hoffmann. "Quantum Interference, Graphs, Walks, and Polynomials." Chemical reviews 118, no. 10 (2018): 4887-4911.

Understanding behaviors and properties of liquid water has been a long-standing topic in both experimental and computational chemistry. Atomic level simulations for water molecules under different circumstances depict microscopic pictures to tackle the problems. We use the normal modes of the optimal structure of a single water molecule as the reference to construct the coordinate systems and then the effective potential energy surfaces of the molecular in the bulk water environment. We use thousands of uncorrelated structures sampled by path integral molecular dynamics. In each structure, we collect the exact frequencies obtained from the effective potential energy surface for each vibrational normal mode. The results hint that the frequency of the symmetric stretching mode is often lower than that of the asymmetric stretching mode. We will also show its implication in the IR and Raman spectra.

Ionic liquids are recognized as the third group of solvents and considered to be environmentally friendly electrolytes due to their nonvolatility, high thermal stability, and high ionic conductivity. Ionic liquid electrolytes based on the pyridinium cation and bis-(fluorosulfonyl)amide anion have been reported to exhibit a good performance for the next generation sodium-ion battery. Here we report a systematic investigation on the influence of counter-cation species to the transport properties of sodium-ion in ionic liquid system using a self-consistent MD/DFT combination to account the strong effect charge transfer and polarization while enabling the simulation to be carried out at ns order. The results suggest that the diffusion of sodium ion is considerably higher in [Na, C₁Pip][FSA] system compared to [Na, C₁Pyr][FSA] owing to the higher charge transfer that effectively reduces the total charges of ionic liquid cation and anion.

Presently, ammonia production is performed by the energy intensive Haber-Bosch process, requiring high temperatures and pressures. While it is possible to electrochemically produce ammonia from nitrogen gas in ambient conditions, the low solubility of nitrogen gas in traditional electrolytes and the competing hydrogen evolution reaction act as two barriers. 

Ionic liquids are suitable electrolytes to counteract both barriers, displaying higher gas solubilities and as a non-aqueous electrolyte, allowing control over reactive hydrogen sources, increasing Faraday efficiencies.¹ Furthermore, the versatility of ionic liquids allows constituent ions to be tweaked for specific properties. 

It has been observed that the fluorination of ionic liquids increases their gas solubility.² However, reasons as to why this is are yet to be fully elucidated. In this work, nitrogen gas solvation is simulated in ionic liquid clusters. In particular, imidazolium and pyrrolidinium based cations C₄mim⁺ and C₄mpyr⁺ are contrasted against their fluorinated counterparts C_FC₃mim⁺ and C_FC₃mpyr⁺, by being paired with dicyanamide anions.

The Fragment Molecular Orbital (FMO) method is combined with the recently developed spin ratio scaled second order Møller–Plesset perturbation theory (SRS-MP2)³ is used to construct minimum energy two ion pair structures of each ionic liquid. Then, nitrogen gas is inserted into these clusters, allowing an quantitative energetic comparison between each ionic liquid. 

The interaction energy between the ionic liquid and nitrogen gas and the deformation of each ionic liquid upon gas insertion separately do not correlate with solubility trends. Instead, the sum of these observables, the binding energy of gas insertion correlates with solubility. Ultimately, this provides a theoretical framework to assess the capacity of ionic liquids to dissolve small gases.

[1] Zhuo et al., Energy Environ. Sci., 2017, 10, 2516

[2] Almantariotis et al., J. Phys. Chem. B, 2017, 121, 426

[3] Tan et al., J. Chem. Phys. 2017, 146, 064108

Time-dependent density functional theory (TD-DFT) is the most accessible method for computationally treating electronic excited states of medium- to large-sized molecular systems. Known limitations inherent in traditional Kohn-Sham DFT unfavourably translate directly into TD-DFT, including poor treatment of noncovalent interactions. Techniques to appropriately treat noncovalent interactions in DFT are well-developed for the electronic ground state but remain largely untested for excited states. 

In this work, we assess the performance of time-dependent density functional approximations (TD-DFA) in treating noncovalent interactions for electronically excited states by the study of excimer and exciplex binding energies. Excimer and exciplex systems are studied specifically, as they combine both excited-state properties and fundamental noncovalent interactions. Consequently, any computational method applied to such systems must be able to describe both. 

While there have been studies of older methods [1]—often based on various experimental or computational reference data—we establish a common reference for all systems against which older and newer methods are benchmarked. A modern wavefunction reference of SCS-CC2/def2-TZVP is established, showing agreement with CCSDR(3) estimated to the complete-basis-set limit. Binding energies and equilibrium distances for a set of selected excimers and exciplexes are thoroughly investigated against this reference for various TD-DFAs. The TD-DFAs studied span across global hybrids, range-separated hybrids, double-hybrids, and newly developed range-separated double-hybrids [2]. We hope this study provides valuable insights for further method development to address noncovalent interactions in electronic excited states.

[1] Huenerbein, R.; Grimme, S. Chem. Phys. 2008, 343, 362–371. 

[2] Casanova-Páez, M.; Dardis, M. B.; Goerigk, L. J. Chem. Theory Comput. 2019. Published online: https://doi.org/10.1021/acs.jctc.9b00013.

Many types of CNT-based functional materials are being developed and are now applied to various devices, such as nano chemical sensors, efficient and durable electrodes for secondary batteries, and flexible organic thermoelectric devices. Their functional properties depend on the properties of CNTs, e.g. length, size, chirality, and number of walls, contained in CNT-based materials, such as CNT yarns, CNT films, or CNT nano-composites. In addition to that, the interface carbon structures in CNT-based materials also determine the properties of their functionalities. However, there are difficulties in direct experimental measurements of the interfacial carbon structure in CNT-based materials because of their structural complexities. Therefore, the theoretical simulation of the interfacial structure is required to predict and design such functional materials. To this end, we here report the multiscale kinetic simulation scheme for interfacial systems to predict their structure and properties and show its application to the interfacial amorphous carbon in CNT-based materials. In our scheme, the energy and gradient calculations are done with the Self-consistent charge density functional tight-binding method and the structural searches are performed by the artificial force induced reaction method combined with the rate constant matrix contraction method which are implemented in the developer version of the GRRM program. The calculated structural transitions of amorphous carbons are then mapped onto the structural transition route map (STRMs) composed of local energy minima (nodes) and transition paths (edges). The constructed STRMs allows us to predict and analyze the interfacial structures relaxation mechanism and resulting functional properties. From the simulations, we found that the interfacial steric constraints have a non-negligible effect on structural relaxation processes of amorphous carbons and discussed the guiding principle of the interfacial structure control. We also discuss the applicability and limits of our simulation scheme. 

Protic ionic liquids (PILs) are synthesised via a simple Brønsted acid-Brønsted base proton transfer reaction. In this work, we study the degree of proton transfer in diamine PILs as a means of quantifying the ionicity of these PILs by using thermodynamic cycles. We focus on four PILs, which are, dimethylethylenediamine acetate [DMEDAH][Ac], dimethylethylenediamine formate [DMEDAH][Form], dimethylethylenediamine propionate [DMEDAH][Prop] and dimethylethylenediamine nitrate [DMEDAH][Nitrate]. We propose an alternative measure, ∆pKa^IL, where we consider the ions of ILs as single molecular entities rather than individual ions. Single and double ion-pairs of PILs were studied to understand the importance of cooperativity effects on influencing the extent of proton transfer. It was found that the single ion-pair model was insufficient to reflect accurate ∆pKa^IL values. Increasing the cluster size from 1 to 2 led to improved ∆pKa^IL. The relative basicity of the anion was found to be a significant factor in including the role of the solvation model as well as the preferred protonation site. PILs consisting of strongly basic anions such as [Ac] or [Form] showed that protonation of both primary and tertiary amine centres was possible to the same degree. Conversely, [Nitrate]-based PILs preferred the tertiary amine centre instead. We argue that the implementation of a solvation model for studying the extent of ionicity in PILs is dependent on the charge distribution of the resulting ionic liquid. We find that gas phase calculations are sufficient to reflect the extent of ionicity in primary protonated PILs.

It is well known that the majority of density-functional approximations (DFAs) suffer from delocalisation error which can be characterised by concave-down fractional charge behaviour (Cohen, Mori-Sanchez & Yang 2008). In 2015, Dale and Johnson observed that DFA calculations conducted with polarizable continuum solvent models (PCM) result in concave-up fractional charge behaviour, interpreted as localisation error (Dale & Johnson 2015). It was suggested that a carefully chosen dielectric constant could return the linear fractional charge behaviour expected of an exact density-functional, consistent with Koopmans' theorem (Perdew et al. 1988). The goal of this work is to construct a procedure for finding an optimised dielectric constant which closely approximates this expected linear behaviour. The optimisation routine is based on the bisection method, converging to linear from both a concave-up and -down fractional charge curves as the dielectric constant is modified. Once the dielectric tuning method was implemented it was tested on the relevant testing sets, specifically the vertical ionisation energy (VIE) set published by McKechnie, Booth, Cohen and Cole (2015). This method shows promise in the linear correction of DFT plots in most cases - particularly hybrid cases where neither delocalisation nor localisation error was extreme. The method, however, tended to return poor results compared to published energetic approximations of VIE using coupled-cluster methods. These results and potential applications of this dielectric tuning method will be discussed.

Recent work in our group has been focused on studying the effect of static electric fields on reaction kinetics and thermodynamics, and to what extent these effects are general and applicable. Up to now, however, the application of electric fields to electronic excited states has been largely confined to Stark spectroscopy, rather than as a usable strategy for deliberately altering excited states. Here, we present a proof-of-concept study into the feasibility of applying static electric fields as a way of tuning photochemical behavior, using charged functional groups (acid/base groups) as the means by which the electric field is applied. We demonstrate that, with acetophenone, the electric field effects are large, usable, and persistent in high-polarity solvents.

Li_x(GeP)₂S₁₂ (LGPS) is a lithium superionic conductor, where an important potential application is an electrolyte for all-solid-state batteries that could be safer and have higher power compared to conventional batteries using liquid electrolytes. Li₁₀GeP₂S₁₂ shows an exceptionally high conductivity of 12 mS/cm at room temperature [1], and doubling of the conductivity to 25 mS/cm was attained in the related compound Li_9.54Si_1.74P_1.44S_11.7Cl_0.3 [2]. The structure of LGPS is complicated. The backbone is a framework of GeS₄ and PS₄ tetrahedra where there are (Ge,P) shared sites and P-only sites. Li is four-folded coordinated with S and occupy four types of sites, Li1 to Li4. (Li1)S₄ and (Li3)S₄ form a one-dimensional chain and this is considered to be the primary Li diffusion route. The original article [1] claimed that the Li1 site is clearly double-split while the other Li sites are not split. However, in our presentation we show that the Li3 site is actually double-split at room temperature and triple-split at 10K. 

The consequence of Li splitting is more local minima for Li, which in turn results in increased complexity in Li migration paths. Understanding and controlling of Li splitting is crucial to further enhance Li conductivity. Both Li1 and Li3 sites, which are found to split, take part in the primary Li conduction path and therefore the intriguing high Li conductivity of LGPS should be strongly influenced by fine details of the Li potential. Our first principles calculations show that that neither Li1 nor Li3 sites splits in Li₁₂Ge₃S₁₂ where all Li sites are occupied. Therefore, reducing the Li concentration, or introducing Li vacancies, was found to be necessary for splitting of these Li sites. 

[1] Nat. Mater. 10, 682 (2011). [2] Nat. Energy, 1, 16030 (2016).

Breslow intermediates, the key intermediates in N-heterocyclic carbene (NHC)-catalyzed reactions, can break the C–N bonds of thiamin and other NHCs, leading to the fragmentation and the 1,3-rearrangement. Distinct reaction pathways, in terms of radical and ionic channels, have been proposed in the literature.^1,2 In this study, we investigate the reaction mechanism of thiamin analogue with density functional theories. Three different protonation states, including the neutral amine, the N1-protonated amine, and the imine, are located. Computational results show that the Breslow intermediate in the protonation states of the neutral amine and of the N1-protonated amine could only undergo the radical route. On the contrary, Breslow intermediate in the imine state could proceed through both of the radical and the ionic channels. Among all of the reaction pathways, the ionic route of the imine state exhibits the lowest free energy barrier (ΔG^ǂ = 22.4 kcal/mol, SMD model³). In the ionic mechanism, however, the C5α–N3' bond cleavage is coupled with a proton transfer from the 4-amine group to the O2'' atom. The reaction mechanism of thiamin with the 4-amine group is therefore concluded ionic, while that of NHCs without a nearby amine group is radical. In addition, the neutral phosphate buffer employed in experiments² tends to facilitate the interchange between the aforementioned tautomers and further affects the reaction pathway afterwards.

Figure 1. Different protonation states (left), and energy profile (right) of the lowest-energy pathway calculated at M06-2X/6-311+G(d,p) level with the SMD model.

References:

1. Alwarsh, S.; Xu, Y.; Qian, S. Y.; McIntosh, M. C. Angew. Chem. Int. Ed. 2016, 55, 55–358.

2. Bielecki, M.; Kluger, R. Angew. Chem. Int. Ed. 2017, 129, 6418–6420.

3. Marenich, A. V.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. B 2009, 113, 6378–6396.

Feynman’s path integral formalism describes nuclei in a quantum system as ”ring polymers”, which describe the closed quantum paths the system can take.  Thermodynamic properties, described in terms of the thermal density matrix, are calculated by sampling all possible paths using Monte Carlo simulation, which are weighted by their action.  The convergence of the method, that is, the number of beads for each ring polymer and the number  of  Monte  Carlo steps  taken,  can  be  improved  by  using  more  accurate  description of the action (Symplectic schemes).  We compare the convergence efficiency between four current existing action formalisms, primitive approximation (PA), Takahashi-Imada (TI), Suzuki factorisation (SF), and Chin formalisms. We further numerically optimised the parameters for SF and CA schemes,  by doing so,  lower order commutators  roughly  cancel  in  order  to  achieve  higher  order  numerical  accuracy and improve the computational efficiency.  We apply the resulting schemes to three realistic systems, H₂O, HCN-HNC, and CH₄.  The first two systems adopted relatively inexpensive however spectroscopically accurate PESs in order to demonstrate the convergence efficiency between four formalisms.  The PES of methane was constructed by using modified Shepard interpolation, that is, as a weighted sum of second order Taylor expansion about a set of PES data points at regions of interest, calculated at a given level of electronic structure theory, the technique for combining modified Shepard interpolation and path integrals formalisms is novel, and we intend to demonstrate that it is efficient and potentially accurate to calculate the total internal energy for systems larger than four atoms.

Single molecule magnets (SMMs) are a broad class of strongly anisotropic inorganic complexes that are promising candidates for use in spintronic devices¹. SMMs adsorbed to sp² surfaces impart hysteresis fingerprints on local electric currents, providing evidence for an exchange interaction between the giant spin of the SMM and the spin of electrons in the medium^2,3. Injecting spin polarised current into SMM-based devices is the next pivotal step towards the realisation of nanomagnet-based spintronics and has become feasible since (i) efficient spin injection in graphene has now been achieved⁴ and (ii) coupling between terbium-based SMMs and quantum dot devices has been demonstrated^2,3. 

We present here⁵ a theoretical investigation of a spintronic device consisting of a SMM grafted to a quantum dot in contact with metallic leads. The SMM is perturbed along its easy axis by the magnetic component of a coherent resonant radiation. We explore the spin dynamics of the SMM and the electric and spin currents flowing through the device when the source electrode is spin polarised. Even at zero bias voltage, we find a net current is pumped through the device and the spin current injected in the ferromagnetic source is switched in the drain lead. Additionally, the source spin current is not only reversed but also amplified in the drain lead. We show that the pumping and related effects can be explained by spin transitions in the SMM induced by the applied radiation and subsequent relaxation via spin asymmetric charge transfer processes.

[1] L. Bogani, and W. Wernsdorfer, Nat. Mater., 2008, 7, 179.

[2] A. Candini, et. al., Nano Lett., 2011, 11, 2634.

[3] M. Urdampilleta, et. al., Nat. Mater., 2011, 10, 502.

[4] W. Han, et. al., Phys. Rev. Lett., 2010, 105, 167202.

[5] K. Hymas and A. Soncini, Accepted by Phys. Rev. B, 2019. 

Nanoclusters of transition metals often exhibit different reactivities from bulk surfaces. For example, sub-nanometric metal clusters have attracted much attention as candidates of alternatives for conventional heterogeneous catalysts. It has been demonstrated that metal clusters can take various isomeric forms under mild conditions. Recently, in several small metal cluster catalysis, the importance of reactivities of metastable isomers has been discussed. 

Here, the next interest would be generality of the importance of metastable isomers. To discuss the relation between these structures and reactivities in various reaction systems, we have systematically investigated catalytic bond activation of NO, N₂, and O₂ on hexamers M₆ of eight transition metals (M = Ni, Cu, Rh, Pd, Ag, Ir, Pt, and Au) by density functional theory calculations. For all the 24 cases, the lowest energy structures at the molecular-adsorption state, bond dissociation transition state (TS), and dissociative-adsorption state were identified by a systematic procedure. Furthermore, using the obtained dataset, a simple linear regression analysis was made to explore the applicability of the Brønsted–Evans–Polanyi (BEP) principle to flexible metal cluster catalysts. The computational details are described in our recent paper (T. Ichino et al., ChemCatChem 2019, 11, 1346-1353). 

The bare M₆ clusters considered here took various geometries (e.g., octahedron for Rh₆, triangular prism for Ir₆, and planar triangle in Au₆). At TS of 20/24 cases, the M₆ moiety changed to similar shapes to metastable isomeric structures in the bare state. The results will expand the generality of the recent discussion that metastable isomers play significant roles in metal cluster catalysis. As the results of simple linear regression analysis, the bond activation energies correlated linearly with the reaction energy changes, demonstrating that the BEP relation exists in the present systems. This result will expand the applicability of the BEP principle to flexible systems.

     The minimum energy conical intersection (MECI) geometries play an important role in photophysics and photochemistry. Especially, the MECI between the singlet ground (S₀) and lowest singlet excited (S₁) states are essential to understand the decay process of photoexcited molecules such as a radiative process emitting fluorescence and a transition to the lowest triplet state via intersystem crossing. Quantum chemical calculations provide various types of S₀/S₁ MECI geometries such as ring strain, ring opening, π-bond rotation, and σ-bond dissociation. Contrary to the equilibrium geometries in the ground and excited states, which can be well understood by the chemical bond theory, the chemical interpretation of MECI geometries is still far from comprehensive understanding.

     In this study, a systematic analysis was performed on the S₀/S₁ MECI of organic molecules.^[1] The frozen orbital analysis, which approximates the excited states with minimal main configurations, was adopted to analyze the excitation energy components at the S₀/S₁ MECI geometries as well as the S₀ and S₁ equilibrium geometries. At the S₀/S₁ MECI geometries, the HOMO−LUMO gaps decreased as expected, but did not vanish. The remaining gaps were balanced with the HOMO−LUMO Coulomb integrals. Furthermore, we discovered that the HOMO−LUMO exchange integrals became approximately zero. Based on the features, we examine a methodology to obtain the molecular geometries of MECI. The new optimization scheme and performance will be explained in the presentation.

[1] H. Nakai, M. Inamori, Y. Ikabata, and Q. Wang, J. Phys. Chem. A, 122, 8905 (2018).

Graphical abstractElectrochemical synthesis holds significant promises in the carbon dioxide conversion to fine and commodity chemicals. Many different electrode materials have been used, with varies product selectivities to alcohols, aldehydes, and hydrocarbons. Boron doped diamond (BDD) is regularly used in redox reactions because it is a metal-free electrode with a wide potential window and low background current.  Nevertheless, the stability of the BDD surface as a function of hydroxyl, oxygen and hydrogen coverage at different electro-potentials have not been studied, and therefore, the reasons for its tendency to convert CO₂ towards low molecular weight aldehydes is unidentified. This work presents the electronic properties of the BDD surface terminated with H, OH, and O species at different coverages in the vacuum and aqueous phase. Additionally, minimum energy pathways of the reaction of CO₂ towards formic acid and formaldehyde were investigated using periodic density functional theory. It will be shown that oxygen species is in average 80 kJ mol^–1 more strongly bound to the surface than H and OH, and that solvation increases the stability of the oxygen covered BDD surface. Therefore, the kinetics of water and hydroxyl dissociation at the BDD surface will play an important role in the CO₂ activation. Additionally, CO₂ reactions at selected oxidised BDD surfaces via formate (CO₂* + H⁺ + e^- → HCOO*), carboxylate (CO₂* + H⁺ + e^- → COOH*) and CO hydrogenation (CO₂* → CO* + O*) will be shown in detail.

The calculation of protein-ligand binding affinities using classical molecular dynamic simulation techniques has the potential to significantly accelerate the drug discovery process. The affinity of a ligand binding to a specific protein is directly related to the difference in free energy between the solvated ligand and the protein-ligand complex. The Automated Topology Builder (ATB, atb.uq.edu.au) has been shown to be able to accurately reproduce the solvation free energies of small molecules. However, the ability of the ATB to accurately predict protein-ligand binding free energies remains to be determined. A set of 8 protein-ligand systems that had been used previously to validate the OPLS and GAFF force fields was selected. Before computing interactions between the ligands and protein the extent to which the experimental binding affinities reflect interactions with the protein, as opposed to simply differences in solvation, was investigated to determine the utility of the test set. This was done by comparing the protein-binding affinities to the 𝜟Ghydration and 𝜟GpartitionH2O→Hexane. It was found that in some cases the systems selected are not a valid test of differences in protein-ligand interactions. For example, in the case of CDK2 the differences in solvation using the ATB parameters are just as predictive as the ligand-protein binding calculations using either OPL3 or GAFF. An analysis of the appropriateness of these test systems will be presented together with the discussion of other challenges associated with the validation of ligand force fields.

Bifurcation is a reaction that gives two products because of a reaction path branching after passing through a transition state [1]. Although intrinsic reaction coordinate (IRC) is widely used in analyses of chemical reactions, bifurcations cannot be described using IRC. It is known that when a　bifurcation occurs, the shape of the potential energy surface perpendicular to the reaction path　changes from a valley to a ridge, which is called valley-ridge transition (VRT). In the previous studies, bifurcations were discussed using ab initio molecular dynamics simulations. Computing frequencies of vibrational modes perpendicular to an IRC path was done to investigate the occurrence of VRT. However, the computational costs of these methods are high. Recently, several automated reaction path search methods have been reported, and analyses of chemical reactions using reaction path networks in which minima and transition states are connected by IRC paths have become possible. In the artificial force induced reaction (AFIR) method [2], one of the automated reaction path search methods, a reaction path is traced by minimizing the model energy function called the AFIR function in which artificial force term between fragments is added to the potential energy function. The minimization path on an AFIR function is called an AFIR path. In the present study, a method to explore bifurcations on a reaction route network by investigating the AFIR paths is proposed. The present method was applied to a Diels-Alder reaction of 2-vinylfuran and 3-methoxycarbonylcyclopentadienone, which has been reported as a reaction accompanying a bifurcation. It was shown that the previously reported bifurcation could be detected using the present method. In addition, some other bifurcations were newly found in the reaction route network of the Diels-Alder reaction. 

[1] P. Valtazanos, K. Ruedenberg, Theoret. Chim. Acta., 1986, 69, 281-307.

[2] S. Maeda, K. Morokuma, J. Chem. Phys., 2010, 132, 241102.

Colossal permittivity (CP) dielectric materials have emerging applications in microelectronics and high-density storage materials. High permittivity and low dielectric loss are the desired characteristics of an optimal performing dielectric material. Achieving both colossal permittivity and low dielectric loss remained a challenge for many years. Nevertheless, a new class of materials were discovered recently which have the ideal dielectric material properties. The discovery of this highly efficient In + Nb doped TiO2 material (INTO) triggered extensive research on new CP materials. However, the applications of these materials are restricted due to the extreme synthetic conditions at the industrial level as compared to small scale laboratory preparation conditions. Therefore, it is necessary to understand the mechanism leading to the colossal permittivity and low loss characteristics of the corresponding materials, in order to achieve the practical applications.

Initially we are focusing on the mechanism of INTO materials, which will be further extended to other CP materials. In fact, a mechanism called Electron Pinned Defect Dipole has already been proposed for the CP behaviour of INTO material. Even though this mechanism seems like a reasonable fit to the nature of the material, there is not much evidence supporting the claim. We are carrying out detailed investigation of the structural and electronic characteristics of the INTO materials out using Density Functional Theory. Band structure calculations and projected charge density analysis depicts the electron hopping over localized states as the origin of the low dielectric loss in these materials.

Type A gamma-aminobutyric acid (GABA_A) receptors belong to the Cys-loop receptor superfamily of ligand gated chloride channels. Various drug design campaigns have succeeded in developing pharmacologically and clinically important drugs that modulate the inhibitory effects of the neurotransmitter GABA on GABA_A receptors. Neurosteroids binding at the transmembrane region of GABA_A have an established therapeutic role in treating behavioural disorders. In order to develop more effective compounds based on the neurosteroid scaffold, we aimed to characterise their binding mode in detail. A recent publication (Chen et al., 2018), points to a neurosteroid binding-site within the alpha1 subunit not previously observed in resolved GABA_A structures. The binding mode of these compounds was studied using carefully equilibrated molecular dynamics simulations performed on the OpenMM GPU-accelerated platform. We calibrated flat-bottom restraints through a series of simulations to establish the balance necessary to maintain the compounds at the binding-site while allowing unbiased sampling. Stable binding modes were identified for the compounds studied herein and we report the important interactions observed during the simulation. This will form the basis for experimental validation of the important binding residues and refinement of the neurosteroid scaffold.

For the development of  magnesium ion batteries the search for a better electrolyte anion is one of the highly challenging tasks. Recently the boron cluster anion, viz., CB₁₁H₁₂^-, has been experimentally shown to have excellent properties as a halogen free anionic component of the electrolyte for Mg ion batteries.^[1] Moreover, highly stable inorganic derivatives of the dodecaborane dianion, namely, B₁₂(CN)₁₂^2- [2] and B₁₂(SCN)₁₂^2- [3] are theoretically predicted to be excellent electrolytes for lithium and magnesium ion batteries. 

In this context, we have theoretically proposed hybrid organic-inorganic derivatives of B₁₂H₁₂^2-, viz., B₁₂X₁₂^2- (X = -C≡C-CN and -C≡C-BO) using density functional theory.^[4] Both B₁₂(C≡C-CN)₁₂^2- and B₁₂(C≡C-BO)₁₂^2- possess high stability in the gas phase. The presence of the organic-inorganic functional group in the B₁₂H₁₂^2-  increases the solubility of B₁₂X₁₂^2- in low polarity solvents. Both B₁₂(C≡C-CN)₁₂^2- and B₁₂(C≡C-BO)₁₂^2- are found even more suitable electrolyte anions than that of the B₁₂(CN)₁₂^2- and B₁₂(SCN)₁₂^2- because Li⁺/Mg²⁺ salt of the former two dianions require less energy to dissociate into corresponding cation and anion in the solvent. In addition, the oxidation potential of B₁₂(C≡C-CN)₁₂^2- and B₁₂(C≡C-BO)₁₂^2- vs Mg²⁺/Mg is very high (12.58  and 12.91 V). Therefore, these dianions are proposed as better electrolytes for reversible Li and Mg ion batteries. Thus the present work shows the possibility of designing desired multiply charged stable anions for appropriate applications through suitable organic-inorganic functionalization.

References

1. O. Tutusaus et al, Angew. Chem., Int. Ed. 2015, 54, 7900.
2. H. Zhao et al,  Angew. Chem., Int. Ed. 2016, 55, 3704.
3. H. Fang et al, J. Phys. Chem. C 2017, 121, 7697.
4. M. Joshi et al, J. Phys. Chem. C 2018, 122, 27947.

Dynamic Kinetic Asymmetric Transformation (DYKAT) involves the conversion of a mixture of enantiomers or a diastereomeric mixture of enantiomers to a single enantiomeric product with quantitative yield and highest enantiomeric excess (>99%). We became interested in addressing the energetic issues of  DYKAT of racemic biaryls accomplishing axial-to-centre chirality transfer.[i] The reaction involves catalytic spiroannulation of 4-(2-bromophenyl)naphthalen-1-ol with diphenylacetylene leading to one of the enantiomeric product with a quaternary stereocenter in high selectivity. We became curious to learn this dual catalytic example[ii] consisting of Pd(OAc)₂ and a chiral N-heterocyclic carbene, along with NaO^tBu and KI in THF as solvent.To gain insights into origin of stereoselectivity, mechanistic investigation was carried out by using the B3LYP-D3 functional. An iodide bound anionic Pd(0)-NHC species with THF-bound Na ion as the counter ion was found to be the most likely active catalyst. The process of dearomatization of phenol ring leading to the formation of a quaternary stereocentre is found to be barrierless when it proceeds through the intermediate formed entirely from the R-biaryl. It was found that intermediate formed from the S-biaryl after migratory insertion is converted to the corresponding intermediate in the R-biaryl pathway through a rotation along C−C biaryl bond.

The donor-acceptor approach has now been extensively used to stabilise molecular fragments (atoms or molecules) of the main group elements to form “molecular materials”. These molecular materials may or may not be stable in their material form. We present here a theoretical investigation to stabilise group 13-15 heteronuclear diatomics with the help of donor ligands (cAAC, NHC). Group 13-15 diatomics are well known in their bulk material form for their use in electronics as semiconductor materials. Stabilising them in their molecular form opens up the potential for possibly a new route of their synthesis (which at present requires very harsh reaction conditions). These molecular materials can also act as a soluble form of the otherwise insoluble bulk material. Our results from a DFT investigation suggests that these diatomics can be stabilised by the use of one donor ligand (there are previously reported studies when these fragments have been stabilised by the use of two donor ligands, which suggests they have a different bonding model as well). The bonding and electronic structures of these systems have been explored by the aid of MO, NBO and EDA analysis. Multireference methods were employed to investigate AlN, which has a multiconfigurational character. 

Fragment Molecular Orbital¹⁾ (FMO) method is one of the powerful computational methods for assisting Structure-Based Drug Design (SBDD). FMO method is considered to give more accurate protein-ligand interaction energies than classical molecular mechanics. FMO also gives Inter-Fragment Interaction Energies (IFIE) easily. Thus, we can explain the interaction energy results easily using IFIE values. 

Although FMO gives plenty of information with regard to interaction energies, analyzing methods are still under development. For example, usually, large numbers of IFIE values are obtained against a smaller number of protein-ligand experimental free energy changes, which presents a so-called n<p problem. Thus, advanced statistical methods are required for solving the problem.

In this study, we applied some statistical methods (PLS and Sparse PLS) to analyze FMO calculation results of DPP4-inhibitor systems, which is one of the antidiabetic drugs and has sufficient PDB data for analyzing the relationships. Using the Sparse PLS, a better correlation coefficient between calculated and experimental pIC50s of the inhibitors were obtained. As a result of this statistical compensation for FMO results, charged amino acids were corrected more than other amino acids. Although this result shows a sufficient correlation between the observed and calculated pIC50s, some of the coefficients of the multiple regression type PLS expression are unexplainable. Thus, we are trying to compensate for the FMO results by SCIFIE²⁾, which corrects overestimated long-range electrostatic interactions. Their details are going to be shown in the presentation.

References

1) Kitaura, K., Ikeo, E., Asada, T., Nakano, T. & Uebayasi, M. Fragment molecular orbital method: an approximate computational method for large molecules. Chem. Phys. Lett. 313, 701–706 (1999).

2) Tanaka, S., Watanabe, C., Okiyama, Y., Statistical correction to effective interactions in the fragment molecular orbital method, Chem. Phys. Lett., 556, 272-277 (2013).

Acetylene is known to be a key reactant in molecular weight growth chemistry of combustion environments. In the well-studied HACA reaction (H loss, C₂H₂ addition), two acetylene molecules add sequentially to a phenyl radical, to form naphthalene. The HACA reaction is observed only at high temperatures, owing to the positive energy barrier to the first acetylene addition. However, low-temperature molecular weight growth reactions are known to be significant in extraterrestrial chemistry, particularly in the interstellar medium and in Titan’s atmosphere. Key formation mechanisms for nitrogen-substituted polycyclic aromatic hydrocarbons (NPAHs) are currently under scrutiny, but could involve the molecular weight growth reactions of both ions and radical species.

Acetylene addition to pyridine- and aniline-based distonic radical cations is reported at room temperature, using ion-trap mass spectrometry. These reactions occur with efficiencies between 0.1% and 40%, with the 3- and 4-dehydroanilinium radical cations reacting 2 orders of magnitude more slowly with acetylene than the 2-dehydroanilinium radical cation, and all three dehydropyridinium radical cations. Preliminary calculations with M06-2X-D3(0)/6-31++G(2df,p) indicate that the energy of the inner, adduct-forming transition state is correlated with the reaction efficiency – acetylene reacts with 3- and 4-dehydroanilinium radical cations through an inner transition state with energy within 0.3 kcal/mol of the separated reactants, whereas the other radical cations react with inner transition states approximately 5 kcal/mol below the energies of the separated reactants. To what extent the inner transition state is ‘submerged’ relative to the reactants may therefore prove critical in identifying reactions that may occur in the low temperature conditions of Titan’s atmosphere.

We present the laboratory synthesized two new cycloalkoxysilanes which have been evaluated as external donors in heterogeneous Ziegler-Natta catalyst for the synthesis of polypropylene. Polymerization of propylene was carried out using 4^th generation Ziegler-Natta (ZN) catalyst containing diisobutylphthalate (DIBP) as an internal donor in conjunction with triethylaluminium (TEAL) as cocatalyst. To exploit the experimental behavior and structural aspects of these new external donors i.e. control of the tacticity and productivity of polypropylene polymer, quantum mechanical calculations (DFT) using B3LYP (Becke-3-parameters,Lee-Yang-Parr) functional were performed on known commercial alkoxysilanes to generate the electronic and structural aspects of external donors then these were implemented over newly synthesized external donors. The theoretical binding energies of complex formed between the external donors and the co-catalyst were found to have a fair correlation with the experimentally measured productivity of polypropylene. The comparative results confirmed that certain essential structural characteristics are required to achieve high activity of catalyst and stereospecificity of polypropylene.

References:

1. M. Gao, H. Liu, J. Wang, C. Li, J. Ma, G. Wei, Polymer, 2004, 45, 2175-2180.
2. G. Singh, S. Kaur, U. Makwana, R. B. Patankar, V. K. Gupta, Macromol. Chem. Phys., 2009, 210, 69-76.
3. A. D. Becke, J. Chem. Phys., 1993, 98, 5648-5652.
4. K. Raghavachari, H. B. Schlegel, J. A. Pople, J. Chem. Phys., 1980, 72, 4654-4655.

It is well known that conventional local-density approximation (LDA) and generalized gradient approximation (GGA) based functionals severely underestimate the band gap of oxides including TiO₂ materials. The broadly used hybrid functionals such as PBE0 and B3LYP give too large calculated band gap values for TiO₂. To avoid so-called band gap problem in DFT and to describe the electronic structure of TiO₂ materials properly, we proposed a modified hybrid functional containing 12.5 % of non-local Fock exchange called as PBEx [1]. Based on this PBEx functional, the prediction of size dependent band alignment in anatase and rutile nanoparticles was investigated [2]. A predictive map of how the anatase-rutile level alignment varies from the smallest nanoparticles to the bulk was provided on the basis of vacuum-referenced electronic levels. In agreement with most recent works, a staggered type II anatase level alignment is predicted for the bulk, which we further find to persist into the regime of large NPs. Our results also suggest that other level alignments which are less favorable for photocatalysis will emerge when the diameter of the TiO₂ NPs is reduced below ~15 nm. 

References

[1] Kyoung Chul Ko, Oriol Lamiel-Garcia, Jin Yong Lee, and Francesc Illas, Phys. Chem. Chem. Phys. 18, 12357 (2016)

[2] Kyoung Chul Ko, Stefan T. Bromley, Jin Yong Lee, and Francesc Illas, J. Phys Chem. Lett. 8, 5593 (2017)

   Excited-state dynamics is attracting much attention in various fields such as bio- and nano-science, for example, from the viewpoint of light-energy conversions and emission processes. In addition to experimental studies, various theoretical approaches have been performed from the microscopic point of view. However, simulations of excited-state dynamical process of practical bio- and/or nano-systems might not be feasible due to the large computational costs. Our research group has developed divide-and-conquer density functional tight-binding molecular dynamics (DC-DFTB-MD) method in order to perform the large-scale simulations in the ground state. The present study extended the DC-DFTB-MD method to time-dependent (TD) theory, as denoted by DC-TDDFTB-MD, to treat excited-state dynamics.

   In the presentation, theoretical background, implementation, and illustrative applications will be explained. Photoactive yellow protein (PYP) (~2000 atoms) exhibits an absorption maximum at 2.78 eV, while the absorption maximum of chromophore occurs at 4.37 eV in water. Thus, the red-shift is 1.59 eV. The excitation energy shift could be reasonably reproduced by the present method as well as the correlation method, namely, DC-TDDFTB (1.46 eV), DC-TDDFT (1.43 eV), DC-SACCI (1.63 eV), respectively. On the other hand, the wall time of DC-TDDFTB was drastically short, i.e., DC-TDDFTB (1.87 seconds), DC-TDDFT (~3 hours), DC-SACCI (~11 hours). The lifetime of 2-acetylindan-1,3-dione (AID) in acetonitrile solvent following the fluorescence could be also demonstrated by the DC-TDDFTB-MD simulations with the use of the all-atom model (~900 atoms) of AID and explicit 150 acetonitrile molecules. 

[1] H. Nishizawa, Y. Nishimura, M. Kobayashi, S. Irle, and H. Nakai, J. Comput. Chem., 37, 1983 (2016).

[2] N. Komoto, T. Yoshikawa, J. Ono, Y. Nishimura, and H. Nakai, J. Chem. Theory Comput., 15, 1719 (2019).

Since its first isolation in 2004, graphene has been extensively studied for its numerous exceptional properties such as its conductivity and mechanical strength.^[1] While its ability to non-covalently bind molecules has been well studied for applications in sensors and extraction devices,^[2] this principle remains surprisingly unexplored for the sake of stabilizing transition structures. Given the current interest in metal-free catalysis,^[3] expanding the application of this concept to transition structures has the potential to open up opportunities for applications of graphene as a catalyst. Herein, we explore the possibility to lower the activation energy of a chemical process purely through stabilizing π-π interactions between transition structure and graphene using density functional theory methods. On the simple example of binaphthyl racemizations we find a significant catalytic effect originating  from π-π interactions and shape-complementarity between catalyst and transition structure indicating the potential for applications of pure graphene in catalysis beyond its use as a catalyst support.

[1] M. J. Allen, V. C. Tung, R. B. Kaner, Chem. Rev. 2010, 110, 132-145.

[2] F. Perreault, A. Fonseca de Faria, M. Elimelech, Chem.Soc.Rev.2015, 44, 5861-5896.

[3] X. Liu and L. Dai, Nat. Rev. Mater. 2016,1, 16064.

Formation of aerosols or clouds in the atmosphere significantly affect climate weather but also human health. We focus on the study of new particle formation in the atmosphere from single molecules. Colliding molecules might form clusters. If those clusters are stable enough, they then grow into aerosol particles. To perform molecules-clusters-aerosol population analysis, precise quantum chemistry calculations are required (calculations of clusters stability). We explain how we deal with obstacles such as proper configurational sampling of atmospheric molecular clusters, performing computationally exhausting quantum chemistry calculations or numerical solving of differential equations for clusters evolution where the concentration of molecules differs by several orders of magnitude. In the end, we present our research in the context of several important molecules/clusters in the atmosphere, e.g., clusters containing sulphuric acid, ammonia, guanidine, water, and other molecules.

Development of selective therapeutics targeting neuronal nicotinic acetylcholine receptors (nAChRs) is a long-sought goal which has been inspired by their established role in devastating neurodegenerative diseases. nAChRs assembled in a 3α:2β stoichiometry contain a third agonist binding site at the α4α4 interface which offers a unique opportunity to develop selective therapeutics. Compounds targeting this site seem to possess a desirable modulatory profile analogous to benzodiazepines targeting GABAA receptors. Two such compounds, CMPI and NS9283 have been proven to bind at the α4α4 agonist binding site using site-directed mutagenesis, yet their precise binding mode is yet to be revealed. We conducted molecular dynamics simulations and free energy perturbation (FEP) calculations to characterise the binding modes of CMPI and NS9283. Carefully equilibrated all-atom simulations, revealed an overlapping binding mode between CMPI and NS9283 at the α4α4 binding site with stable interactions to residues of established importance. For further validation and to establish a platform for future lead optimisation, we attempted to correlate experimentally derived potencies with the relative binding free energies of CMPI and NS9283 analogues calculated using FEP. The findings and protocols reported herein should contribute to the development selective nAChR therapeutics.

The exact wave function of two-electron atoms can, as proposed by Fock¹, be expressed as a series expansion in the hyperradius r as

Ψ   =   Σ_h r^h · Ψ_h(ln(r),α,d)   =   Σ_h r^h Σ_p ln(r)^p · ψ_hp(α,d).

The challenge lies in deriving the Fock coefficients ψ_hp(α,d), which depend on the hyperangle α and the scaled interelectron distance d, as well as - parametrically - on the electron and nucleus charges, Y and Z, and the energy E.

Assuming that the ground state energy E can be expressed as a power series in the parameter Y, E = ε₀Y⁰+ε₁Y¹+ε₂Y²+..., turns the Fock coefficients into power series in Y (and, less importantly, Z), and thus opens the possibility of calculating the terms of the exact wave function following the ideas of perturbation theory. Treating the components ε_y of the energy separately allows for a massive simplification of the analytical expression of the wave function.

This presentation demonstrates the methods for obtaining the terms of the exact wave function which correspond to the first-order perturbation correction, and shows how the coefficients of the pure Fock expansion can be derived using the tools of perturbation theory.

[1] V. Fock, Nor. Vidensk. Selsk. Forh.31, 138 (1958) 

Recent experimental results show that intrinsic defects are present even in high quality semiconducting transition metal dichalcogenides (TMDs) such as MoTe₂. Some of the defects manifest themselves as true atomic lattice distortions with a several nanometer spatial extent, an unexpected finding in semiconducting TMDs. Additionally, these defects appear to be associated with magnetic properties and might thus be desirable for specific applications such as spintronics. However, the nature of the defects and the origin of the several nanometer-scale lattice distortions remains unknown. In this contribution, we use periodic density functional theory calculations to gain insights into the features of these defects. In particular, by comparing computed local density of states plots to experimental scanning tunneling microscopy images, we find that the defects are likely to be antisite defects in which Mo atoms replace chalcogen atoms. Additionally, we compute phonon spectra of the defective structures and compare them to the phonon spectrum of the pristine material to determine whether the hypothesized defects can be responsible for the lattice distortions observed in the experiments.

Scaffolds of molecules play a critical role in determining their molecular properties. Thus, generating molecules retaining a specific scaffold as a substructure has practical advantages in molecular design, for instance, in drug discovery. Accordingly, we developed a scaffold-based molecular graph generative model. The model generates new molecular graphs by extending the graph of a scaffold through successive additions of atoms and bonds. In contrast to previous related models, our model guarantees that the generated molecules have the scaffold as a substructure. 

The model showed high validity, uniqueness, and novelty of generated molecules, showing that the model can learn chemical rules of adding atoms and bonds rather than simply memorizing the training set. We also tested that our model can generate molecules with desirable properties. Despite the fact that the scaffold restricts the search space, our model successfully generated new molecules with a desirable molecular property while retaining a scaffold. Moreover, the model can simultaneously control multiple molecular properties of generated molecules. We further tested that scaffold-based generation strategy is applicable for designing epidermal growth factor receptor inhibitor (EGFR) where only a small amount of labeled data is available. We trained the model with both a small amount of labeled data and a large amount of unlabeled data in a semi-supervised manner. As a result, the model designed new potential EGFR inhibitors whose predicted binding affinity is about 1.5 higher than those of their scaffolds in terms of pIC50. 

Mutations in neurotransmitter transporters in the SLC6 family  have been implicated in a range of psychiatric disorders including ADHD, depression, Parkinsons and  addiction, rendering them attractive targets for studies into mental disorders. Interactions between  these lipids and embedded membrane proteins are known to play a regulatory role with regards to protein activity,   localisation and trafficking. Due to the complexity of natural membranes, most membrane proteins have been investigated in  the context of simplified model bilayers containing only a few key lipid species. While this reduces the complexity of system set up,  it is unclear whether the omitted lipid species play critical roles in protein modulation.

Using coarse grained molecular dynamics simulations of the dopamine, serotonin and glycine transporter proteins in a complex model of the neuronal membrane, and in a two-component POPC-cholesterol membrane, we investigated how lipid composition affects physical membrane properties such as membrane thickness  and fluidity. In addition, analysis of how different lipid species cluster around the protein through density calculations provides pertinent  information on the kind of lipid-proteins taking place within these simulated systems.