Quantum computing in pharma: A multilayer embedding approach for near future applications.

Quantum computers are special purpose machines that are expected to be particularly useful in simulating strongly correlated chemical systems. The quantum computer excels at treating a moderate number of orbitals within an active space in a fully quantum mechanical manner. We present a quantum phase estimation calculation on F2 in a (2,2) active space on Rigetti's Aspen-11 QPU. While this is a promising start, it also underlines the need for carefully selecting the orbital spaces treated by the quantum computer. In this work, a scheme for selecting such an active space automatically is described and simulated results obtained using both the quantum phase estimation (QPE) and variational quantum eigensolver (VQE) algorithms are presented and combined with a subtractive method to enable accurate description of the environment. The active occupied space is selected from orbitals localized on the chemically relevant fragment of the molecule, while the corresponding virtual space is chosen based on the magnitude of interactions with the occupied space calculated from perturbation theory. This protocol is then applied to two chemical systems of pharmaceutical relevance: the enzyme [Fe] hydrogenase and the photosenzitizer temoporfin. While the sizes of the active spaces currently amenable to a quantum computational treatment are not enough to demonstrate quantum advantage, the procedure outlined here is applicable to any active space size, including those that are outside the reach of classical computation.

Chemical Bonding and Bonding Models of Main-Group Compounds.

The focus of this review is the presentation of the most important aspects of chemical bonding in molecules of the main group atoms according to the current state of knowledge. Special attention is given to the difference between the physical mechanism of covalent bond formation and its description with chemical bonding models, which are often confused. This is partly due to historical reasons, since until the development of quantum theory there was no physical basis for understanding the chemical bond. In the absence of such a basis, chemists developed heuristic models that proved extremely valuable for understanding and predicting experimental studies. The great success of these simple models and the associated rules led to the fact that the model conceptions were regarded as real images of physical reality. The complicated world of quantum theory, which eludes human imagination, made it difficult to link heuristic models of chemical bonding with quantum chemical knowledge. In the early days of quantum chemistry, some suggestions were made which have since proved untenable. In recent decades, there has been a stormy development of quantum chemical methods, which are not limited to the quantitative accuracy of the calculated properties. Also, methods have been developed where the experimentally developed models can be quantitatively expressed and visually represented using mathematically well-defined terms that are derived from quantum chemical calculations. The calculated numbers may however not be measurable values. Nevertheless, as orientation data for the interpretation and classification of experimental findings as well as a guideline for new experiments, they form a coordinate system that defines the multidimensional world of chemistry, which corresponds to the Hilbert space formalism of physics. The nonmeasurability of model values is not a weakness of chemistry but a characteristic by which the infinite complexity of the material world becomes scientifically accessible and very useful for chemical research. This review examines the basis of the commonly used quantum chemical methods for calculating molecules and for analyzing their electronic structure. The bonding situation in selected representative molecules of main-group atoms is discussed. The results are compared with textbook knowledge of common chemistry.

The Valence Orbitals of the Alkaline-Earth Atoms.

Quantum chemical calculations of the alkaline-earth oxides, imides and dihydrides of the alkaline-earth atoms (Ae=Be, Mg, Ca, Sr, Ba) and the calcium cluster Ca6 H9 [N(SiMe3 )2 ]3 (pmdta)3 (pmdta=N,N,N',N'',N''-pentamethyldiethylenetriamine) have been carried out by using density functional theory. Analysis of the electronic structures by charge and energy partitioning methods suggests that the valence orbitals of the lighter atoms Be and Mg are the (n)s and (n)p orbitals. In contrast, the valence orbitals of the heavier atoms Ca, Sr and Ba comprise the (n)s and (n-1)d orbitals. The alkaline-earth metals Be and Mg build covalent bonds like typical main-group elements, whereas Ca, Sr and Ba covalently bind like transition metals. The results not only shed new light on the covalent bonds of the heavier alkaline-earth metals, but are also very important for understanding and designing experimental studies.

d-d Dative Bonding Between Iron and the Alkaline-Earth Metals Calcium, Strontium, and Barium.

Double deprotonation of the diamine 1,1'-(tBuCH2 NH)-ferrocene (1-H2 ) by alkaline-earth (Ae) or EuII metal reagents gave the complexes 1-Ae (Ae=Mg, Ca, Sr, Ba) and 1-Eu. 1-Mg crystallized as a monomer while the heavier complexes crystallized as dimers. The Fe⋅⋅⋅Mg distance in 1-Mg is too long for a bonding interaction, but short Fe⋅⋅⋅Ae distances in 1-Ca, 1-Sr, and 1-Ba clearly support intramolecular Fe⋅⋅⋅Ae bonding. Further evidence for interactions is provided by a tilting of the Cp rings and the related 1 H NMR chemical-shift difference between the Cp α and ß protons. While electrochemical studies are complicated by complex decomposition, UV/Vis spectral features of the complexes support Fe→Ae dative bonding. A comprehensive bonding analysis of all 1-Ae complexes shows that the heavier species 1-Ca, 1-Sr, and 1-Ba possess genuine Fe→Ae bonds which involve vacant d-orbitals of the alkaline-earth atoms and partially filled d-orbitals on Fe. In 1-Mg, a weak Fe→Mg donation into vacant p-orbitals of the Mg atom is observed.

Influence of charge transfer on the isomerisation of stilbene derivatives for application in cancer therapy.

The photoisomerisation of non-toxic trans-combretastatin CA4 to its cytotoxic cis isomer demonstrates the high potential of this and similar compounds for localised cancer therapy. The introduction of intramolecular charge-transfer character by altering the substituents of combretastatin systems opens up possibilities to tailor these stilbene derivatives to the special demands of anticancer drugs. In this TDDFT study we explore how absorption wavelengths for both the trans and cis isomers can be red shifted to enable deeper light penetration into tissue and how the trans → cis and cis → trans isomerisations are affected by charge transfer effects to different degrees.

The hypothiocyanite radical OSCN and its isomers.

A biologically relevant reactive sulfur species (RSS), the hypothiocyanite radical OSCN, is generated in the gas phase through flash vacuum pyrolysis (FVP) of trifluoromethyl sulfinyl cyanide CF3S(O)CN at ca. 1000 K. Upon UV light irradiation (365 nm), OSCN rearranges to novel isomers OSNC and SOCN, and further visible light irradiation (400 ± 20 nm) leads to reverse isomerization. The identification of OSCN, OSNC, and SOCN in cryogenic matrices (Ar and N2, 2.8 K) with IR spectroscopy is supported by quantum chemical calculations up to the CCSD(T)-F12/VTZ-F12 level. The potential energy surface for the interconversion of OSCN isomers and their bonding properties are computationally explored by using the CCSD(T)-F12/VTZ-F12 and EDA-NOCV methods, respectively.

Donor-acceptor bonding in novel low-coordinated compounds of boron and group-14 atoms C-Sn.

A summary of theoretical and experimental work in the area of low-coordinated compounds of boron and group-14 atoms C-Sn in the last decade is presented. The focus of the account lies on molecules EL2, E2L2 and E3L3, which possess dative bonds between one, two or three atoms E and σ-donor ligands L that stabilize the atoms E through L→E donor-acceptor interactions. The interplay between theory and experiment provides detailed insight into the bonding situation of the molecules, which serves as guideline for the synthesis of molecules that possess unusual bonding motifs.

Synthesis, Characterization, and Computational Analysis of the Dialanate Dianion, [H3 Al-AlH3 ]2- : A Valence Isoelectronic Analogue of Ethane.

The first example of a well-defined binary, low-oxidation-state aluminum hydride species that is stable at ambient temperature, namely the dianion in [{(Dep Nacnac)Mg}2 (µ-H)]2 [H3 Al-AlH3 ] (Dep Nacnac=[(DepNCMe)2 CH]- , Dep=2,6-diethylphenyl), has been prepared via a magnesium(I) reduction of the alanate complex, (Dep Nacnac)Mg(µ-H)3 AlH(NEt3 ). An X-ray crystallographic analysis has shown the compound to be a contact ion complex, which computational studies have revealed to be the source of the stability of the aluminum(II) dianion.

Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments.

The viroporin p7 of the hepatitis C virus forms multimeric channels eligible for ion transport across the endoplasmic reticulum membrane. Currently the subject of many studies and discussion, the molecular assembly of the ion channel and the structural characteristics of the p7 monomer are not yet fully understood. Structural investigation of p7 has been carried out only in detergent environments, making the interpretation of the experimental results somewhat questionable. Here, we analyze by means of molecular dynamics simulations the structure of the p7 monomer as a function of its sequence, initial conformation and environment. We investigate the conductance properties of three models of a hexameric p7 ion channel by examining ion translocation in a pure lipid bilayer. It is noteworthy that although none of the models reflects the experimentally observed trend to conduct preferentially cations, we were able to identify the position and orientation of titratable acidic or basic residues playing a crucial role in ion selectivity and in the overall conductance of the channel. In addition, too compact a packing of the monomers leads to channel collapse rather than formation of a reasonable pore, amenable to ion translocation. The present findings are envisioned to help assess the physiological relevance of p7 ion channel models consisting of multimeric structures obtained in non-native environments.

The fate of NHC-stabilized dicarbon.

The attempted synthesis of NHC-stabilized dicarbon (NHC=C=C=NHC) through deprotonation of a doubly protonated precursor ([NHC-CH=CH-NHC](2+) ) is reported. Rather than deprotonation, a clean reduction to NHC=CH-CH=NHC is observed with a variety of bases. The apparent resistance towards deprotonation to the target compound led to a reinvestigation of the electronic structure of NHC→CC←NHC, which showed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO/LUMO) gap is likely too small to allow for isolation of this species. This is in contrast to the recent isolation of the cyclic alkylaminocarbene analogue (cAAC=C=C=cAAC), which has a large HOMO-LUMO gap. A detailed theoretical study illuminates the differences in electronic structures between these molecules, highlighting another case of the potential advantages of using cAAC rather than NHC as a ligand. The bonding analysis suggests that the dicarbon compounds are well represented in terms of donor-acceptor interactions L→C2 ←L (L=NHC, cAAC).

Direct estimate of the internal π-donation to the carbene centre within N-heterocyclic carbenes and related molecules.

Fifteen cyclic and acylic carbenes have been calculated with density functional theory at the BP86/def2-TZVPP level. The strength of the internal X→p(π) π-donation of heteroatoms and carbon which are bonded to the C(II) atom is estimated with the help of NBO calculations and with an energy decomposition analysis. The investigated molecules include N-heterocyclic carbenes (NHCs), the cyclic alkyl(amino)carbene (cAAC), mesoionic carbenes and ylide-stabilized carbenes. The bonding analysis suggests that the carbene centre in cAAC and in diamidocarbene have the weakest X→p(π) π-donation while mesoionic carbenes possess the strongest π-donation.

One-electron-mediated rearrangements of 2,3-disiladicarbene.

A disiladicarbene, (Cy-cAAC)2Si2 (2), was synthesized by reduction of Cy-cAAC:SiCl4 adduct with KC8. The dark-colored compound 2 is stable at room temperature for a year under an inert atmosphere. Moreover, it is stable up to 190 °C and also can be characterized by electron ionization mass spectrometry. Theoretical and Raman studies reveal the existence of a Si═Si double bond with a partial double bond between each carbene carbon atom and silicon atom. Cyclic voltammetry suggests that 2 can quasi-reversibly accept an electron to produce a very reactive radical anion, 2(•-), as an intermediate species. Thus, reduction of 2 with potassium metal at room temperature led to the isolation of an isomeric neutral rearranged product and an anionic dimer of a potassium salt via the formation of 2(•-).

Formation of a 1,4-diamino-2,3-disila-1,3-butadiene derivative.

A 1,4-diamino-2,3-disila-1,3-butadiene derivative of composition (Me2-cAAC)2(Si2Cl2) (Me2-cAAC = :C(CMe2)2(CH2)N-2,6-iPr2C6H3) was synthesized by reduction of the Me2-cAAC:SiCl4 adduct with KC8. This compound is stable at 0 °C for 3 months in an inert atmosphere. Theoretical studies reveal that the silicon atoms exhibit pyramidal coordination, where the Cl-Si-Si-Cl dihedral angle is twisted by 43.3° (calcd 45.9°). The two silicon-carbon bonds are intermediates between single and double Si-C bonds due to twisting of the C-Si-Si-C dihedral angle (163.6°).

Comparative study of phosphine and N-heterocyclic carbene stabilized Group†13 adducts [L(EH3)] and [L2(E2H(n))].

Quantum chemical calculations using density functional theory at the BP86/TZ2P level have been carried out to determine the geometries and stabilities of Group 13 adducts [(PMe3)(EH3)] and [(PMe3)2(E2H(n))] (E = B-In; n = 4, 2, 0). The optimized geometries exhibit, in most cases, similar features to those of related adducts [(NHC(Me))(EH3)] and [(NHC(Me))2(E2H(n))] with a few exceptions that can be explained by the different donor strengths of the ligands. The calculations show that the carbene ligand L = NHC(Me) (:C(NMeCH)2) is a significantly stronger donor than L = PMe3. The equilibrium geometries of [L(EH3)] possess, in all cases, a pyramidal structure, whereas the complexes [L2(E2H4)] always have an antiperiplanar arrangement of the ligands L. The phosphine ligands in [(PMe3)2(B2H2)], which has Cs symmetry, are in the same plane as the B2H2 moiety, whereas the heavier homologues [(PMe3)2(E2H2)] (E = Al, Ga, In) have Ci symmetry in which the ligands bind side-on to the E2H2 acceptor. This is in contrast to the [(NHC(Me))2(E2H2)] adducts for which the NHC(Me) donor always binds in the same plane as E2H2 except for the indium complex [(NHC(Me))2(In2H2)], which exhibits side-on bonding. The boron complexes [L2(B2)] (L = PMe3 and NHC(Me)) possess a linear arrangement of the LBBL moiety, which has a B≡B triple bond. The heavier homologues [L2(E2)] have antiperiplanar arrangements of the LEEL moieties, except for [(PMe3)2(In2)], which has a twisted structure in which the PInInP torsion angle is 123.0°. The structural features of the complexes [L(EH3)] and [L2(E2H(n))] can be explained in terms of donor-acceptor interactions between the donors L and the acceptors EH3 and E2H(n), which have been analyzed quantitatively by using the energy decomposition analysis (EDA) method. The calculations predict that the hydrogenation reaction of the dimeric magnesium(I) compound L'MgMgL' with the complexes [L(EH3)] is energetically more favorable for L = PMe3 than for NHC(Me).

Measuring Electron Correlation: The Impact of Symmetry and Orbital Transformations.

In this perspective, the various measures of electron correlation used in wave function theory, density functional theory and quantum information theory are briefly reviewed. We then focus on a more traditional metric based on dominant weights in the full configuration solution and discuss its behavior with respect to the choice of the N-electron and the one-electron basis. The impact of symmetry is discussed, and we emphasize that the distinction among determinants, configuration state functions and configurations as reference functions is useful because the latter incorporate spin-coupling into the reference and should thus reduce the complexity of the wave function expansion. The corresponding notions of single determinant, single spin-coupling and single configuration wave functions are discussed and the effect of orbital rotations on the multireference character is reviewed by analyzing a simple model system. In molecular systems, the extent of correlation effects should be limited by finite system size and in most cases the appropriate choices of one-electron and N-electron bases should be able to incorporate these into a low-complexity reference function, often a single configurational one.

Perspective on the Current State-of-the-Art of Quantum Computing for Drug Discovery Applications.

Computational chemistry is an essential tool in the pharmaceutical industry. Quantum computing is a fast evolving technology that promises to completely shift the computational capabilities in many areas of chemical research by bringing into reach currently impossible calculations. This perspective illustrates the near-future applicability of quantum computation of molecules to pharmaceutical problems. We briefly summarize and compare the scaling properties of state-of-the-art quantum algorithms and provide novel estimates of the quantum computational cost of simulating progressively larger embedding regions of a pharmaceutically relevant covalent protein-drug complex involving the drug Ibrutinib. Carrying out these calculations requires an error-corrected quantum architecture that we describe. Our estimates showcase that recent developments on quantum phase estimation algorithms have dramatically reduced the quantum resources needed to run fully quantum calculations in active spaces of around 50 orbitals and electrons, from estimated over 1000 years using the Trotterization approach to just a few days with sparse qubitization, painting a picture of fast and exciting progress in this nascent field.

Structures and stabilities of group 13 adducts [(NHC)(EX3)] and [(NHC)2(E2X(n))] (E=B to In; X=H, Cl; n=4, 2, 0; NHC=N-heterocyclic carbene) and the search for hydrogen storage systems: a theoretical study.

Quantum chemical calculations using density functional theory at the BP86/TZVPP level and ab initio calculations at the SCS-MP2/TZVPP level have been carried out for the group 13 complexes [(NHC)(EX(3))] and [(NHC)(2)(E(2)X(n))] (E=B to In; X=H, Cl; n=4, 2, 0; NHC=N-heterocyclic carbene). The monodentate Lewis acids EX(3) and the bidentate Lewis acids E(2) X(n) bind N-heterocyclic carbenes rather strongly in donor-acceptor complexes [(NHC)(EX(3))] and [(NHC)(2)(E(2)X(n))]. The equilibrium structures of the bidentate complexes depend on the electronic reference state of E(2)X(n), which may vary for different atoms E and X. All complexes [(NHC)(2)(E(2)X(4))] possess C(s) symmetry in which the NHC ligands bind in a trans conformation to the group 13 atoms E. The complexes [(NHC)(2)(E(2)H(2))] with E=B, Al, Ga have also C(s) symmetry with a trans arrangement of the NHC ligands and a planar CE(H)E(H)C moiety that has a E=E π bond. In contrast, the indium complex [(NHC)(2)(In(2) H(2))] has C(i) symmetry with pyramidal-coordinated In atoms in which the hydrogen atoms are twisted above and below the CInInC plane. The latter C(i) form is calculated for all chloride systems [(NHC)(2)(E(2)Cl(2))], but the boron complex [(NHC)(2)(B(2)Cl(2))] deviates only slightly from C(s) symmetry. The B(2) fragment in the linear coordinated complex [(NHC)(2)(B(2))] has a highly excited (3)(1)Σ(g)(-) reference state, which gives an effective B≡B triple bond with a very short interatomic distance. The heavier homologues [(NHC)(2)(E(2))] (E=Al to In) exhibit a anti-periplanar arrangement of the NHC ligands in which the E(2) fragments have a (1)(1) Δ(g) reference state and an E=E double bond. The calculated energies suggest that the dihydrogen release from the complexes [(NHC)(EH(3))] and [(NHC)(2)(E(2)H(n))] becomes energetically more favourable when atom E becomes heavier. The indium complexes should therefore be the best candidates of the investigated series for hydrogen-storage systems that could potentially deliver dihydrogen at close to ambient temperature. The hydrogenation reaction of the dimeric magnesium(I) compound [LMgMgL] (L=ß-diketiminate) with [(NHC)(EH(3))] becomes increasingly exothermic with the trend B

Preparation, characterization, and theoretical analysis of group 14 element(I) dimers: a case study of magnesium(I) compounds as reducing agents in inorganic synthesis.

A synthetic route to the new amidine (DipNH)(DipN)C(C(6)H(4)Bu(t)-4) (ButisoH; Dip = C(6)H(3)Pr(i)(2)-2,6) has been developed. Its deprotonation with either LiBu(n) or KN(SiMe(3))(2) yields the amidinate complexes [M(Butiso)] (M = Li or K). Their reactions with group 14 element halides/pseudohalides afford the heteroleptic group 14 complexes [(Butiso)SiCl(3)], [(Butiso)ECl] (E = Ge or Sn), and [{(Butiso)Pb(µ-O(3)SCF(3))(THF)}(∞)], all of which have been crystallographically characterized. In addition, the synthesis and spectroscopic characterization of the homoleptic complex [Pb(Butiso)(2)] is reported. Reductions of the heteroleptic complexes with a soluble magnesium(I) dimer, [{((Mes)Nacnac)Mg}(2)] ((Mes)Nacnac = [(MesNCMe)(2)CH](-); Mes = mesityl), have given moderate-to-high yields of the group 14 element(I) dimers [{(Butiso)E}(2)] (E = Si, Ge, or Sn), the X-ray crystallographic studies of which reveal trans-bent structures. The corresponding lead(I) complex could not be prepared. Comprehensive spectroscopic and theoretical analyses of [{(Butiso)E}(2)] have allowed their properties to be compared. All complexes possess E-E single bonds and can be considered as intramolecularly base-stabilized examples of ditetrelynes, REER. Taken as a whole, this study highlights the synthetic utility of soluble and easy to prepare magnesium(I) dimers as valuable alternatives to the harsh, and often insoluble, alkali-metal reducing agents that are currently widely employed in the synthesis of low-oxidation-state organometallic/inorganic complexes.

On the stability, electronic structure, and nonlinear optical properties of HXeOXeF and FXeOXeF.

The electronic ground state, stability, and linear and nonlinear optical properties of HXeOXeF and FXeOXeF have been studied theoretically by employing complete active space valence bond (CASVB), multistate complete active space perturbation theory (MS-CASPT2), and coupled cluster methods. It is shown that the oxygen inserted between the two Xe atoms significantly modifies the ground-state electronic configuration of the formed derivative by increasing the closed-shell contribution (σ(2)) and removing the diradicaloid character observed in HXe(2)F. The electronic charge distribution has been analyzed by employing the atoms-in-molecules (AIM) method. The dissociation channels of HXeOXeF and FXeOXeF have been studied in detail. It was found that these compounds are metastable, protected by substantial energy barriers and, thus, they can be prepared under appropriate conditions. Both two- and three-body dissociation reactions have been considered. The effects of inserting O in HXe(2)F and substituting H (HXeOXeF) by F, leading to FXeOXeF, on the energy barriers are discussed. The significant effects of the inserted oxygen on the polarizability and even more on the first hyperpolarizability have been computed and rationalized.