Qubit Count Reduction by Orthogonally Constrained Orbital Optimization for Variational Quantum Excited-State Solvers.

We propose a state-averaged orbital optimization scheme for improving the accuracy of excited states of the electronic structure Hamiltonian for use on near-term quantum computers. Instead of parameterizing the orbital rotation operator in the conventional fashion as an exponential of an antihermitian matrix, we parameterize the orbital rotation as a general partial unitary matrix. Whereas conventional orbital optimization methods minimize the state-averaged energy using successive Newton steps of the second-order Taylor expansion of the energy, the method presented here optimizes the state-averaged energy using an orthogonally constrained gradient projection method that does not require any expansion approximations. Through extensive benchmarking of the method on various small molecular systems, we find that the method is capable of producing more accurate results than fixed basis FCI while simultaneously using fewer qubits. In particular, we show that for H2, the method is capable of matching the accuracy of FCI in the cc-pVTZ basis (56 qubits) while only using 14 qubits.

Discovery of highly efficient CRBN-recruiting HPK1-PROTAC as a potential chemical tool for investigation of scaffolding roles in TCR signaling.

Hematopoietic progenitor kinase 1 (HPK1, MAP4K1) is a promising target for immune-oncology therapy. It has been recently demonstrated that loss of HPK1 kinase activity can enhance T cell receptor (TCR) signaling. However, many essential functions mediated by the HPK1 scaffolding role are still beyond the reach of any kinase inhibitor. Proteolysis targeting chimera (PROTAC) has emerged as a promising strategy for pathogenic proteins degradation with the characteristics of rapid, reversible, and low-cost versus RNA interference or DNA knock-out technology. Herein we first disclosed the design, synthesis, and evaluation of a series of thalidomide-based PROTAC molecules and identified B1 as a highly efficient HPK1 degrader with DC50 value of 1.8 nM. Further mechanism investigation demonstrated that compound B1 inhibits phosphorylation of the SLP76 protein with IC50 value of 496.1 nM, and confirmed that B1 is a bona fide HPK1-PROTAC degrader. Thus, this study provides a basis for HPK1 degraders development and the candidate could be used as a potential chemical tool for further investigation of the kinase-independent signaling of HPK1 in TCR.

Thiacalix[4]arene-Protected Silver Nanoclusters Encapsulating Different Two-Electron Superatom Oligomers.

The subvalent silver kernel represents the nascent state of silver cluster formation, yet the growth mechanism has long been elusive. Herein, two silver nanoclusters (Ag30 and Ag34) coprotected by TC4A4- (H4TC4A = p-tert-butylthiacalix[4]arene) and TBPMT- (TBPMTH = 4-tert-butylbenzenemethanethiol) containing 6e and 4e silver kernels are synthesized and characterized. The trimer of the 2e superatom Ag14 kernel in Ag30 is built from a central Ag6 octahedron sandwiched by two orthogonally oriented Ag5 trigonal bipyramids through sharing vertexes, whereas a double-octahedral Ag10 kernel in Ag34 is a dimer of 2e superatoms. They manifest disparate polyhedron fusion growth patterns at the beginning of the silver cluster formation. Their excellent solution stabilities are contributed by the multisite and multidentate coordination fashion of TC4A4- and the special valence electron structures. This work demonstrates the precise control of silver kernel growth by the solvent strategy and lays a foundation for silver nanocluster application in photothermal conversion.

Coordinate Descent Full Configuration Interaction for Excited States.

An efficient excited state method, named xCDFCI, in the configuration interaction framework is proposed. xCDFCI extends the unconstrained nonconvex optimization problem in coordinate descent full configuration interaction (CDFCI) to a multicolumn version for low-lying excited states computation. The optimization problem is addressed via a tailored coordinate descent method. In each iteration, a determinant is selected based on an approximated gradient, and coefficients of all states associated with the selected determinant are updated. A deterministic compression is applied to limit memory usage. We test xCDFCI applied to H2O and N2 molecules under the cc-pVDZ basis set. For both systems, five low-lying excited states in the same symmetry sector are calculated, together with the ground state. xCDFCI also produces accurate binding curves of the carbon dimer in the cc-pVDZ basis with chemical accuracy, where the ground state and four excited states in the same symmetry sector are benchmarked.

Monoarsine-protected icosahedral cluster [Au13(AsPh3)8Cl4]+: comparative studies on ligand effect and surface reactivity with its stibine analogue.

Ligand shells of gold nanoclusters play important roles in regulating their molecular and electronic structures. However, the similar but distinct impacts of the homologous analogues of the protecting ligands remain elusive. The C2v symmetric monoarsine-protected cluster [Au13(AsPh3)8Cl4]+ (Au13As8) was facilely prepared by direct reduction of (Ph3As)AuCl with NaBH4. This cluster is isostructural with its previously reported stibine analogue [Au13(SbPh3)8Cl4]+ (Au13Sb8), enabling a comparative study between them. Au13As8 exhibits a blue-shifted electronic absorption band, and this is probably related to the stronger π-back donation interactions between the Au13 core and AsPh3 ligands, which destabilize its superatomic 1P and 1D orbitals. In comparison to the thermodynamically less stable Au13Sb8, Au13As8 achieves a better trade-off between catalytic stability and activity, as demonstrated by its excellent catalytic performance towards the aldehyde-alkyne-amine (A3) coupling reaction. Moreover, the ligand exchange reactions between Au13As8 with phosphines, as exemplified by PPh3 and Ph2P(CH2)2PPh2, suggest that Au13As8 may be a good precursor cluster for further cluster preparation through the "cluster-to-cluster" route.

Improving the Accuracy of Variational Quantum Eigensolvers with Fewer Qubits Using Orbital Optimization.

Near-term quantum computers will be limited in the number of qubits on which they can process information as well as the depth of the circuits that they can coherently carry out. To date, experimental demonstrations of algorithms such as the Variational Quantum Eigensolver (VQE) have been limited to small molecules using minimal basis sets for this reason. In this work we propose incorporating an orbital optimization scheme into quantum eigensolvers wherein a parametrized partial unitary transformation is applied to the basis functions set in order to reduce the number of qubits required for a given problem. The optimal transformation is found by minimizing the ground state energy with respect to this partial unitary matrix. Through numerical simulations of small molecules up to 16 spin orbitals, we demonstrate that this method has the ability to greatly extend the capabilities of near-term quantum computers with regard to the electronic structure problem. We find that VQE paired with orbital optimization consistently achieves lower ground state energies than traditional VQE when using the same number of qubits and even frequently achieves lower ground state energies than VQE methods using more qubits.

Ag22 Nanoclusters with Thermally Activated Delayed Fluorescence Protected by Ag/Cyanurate/Phosphine Metallamacrocyclic Monolayers through In-Situ Ligand Transesterification.

The composition of protection monolayer exerts great influence on the molecular and electronic structures of atomically precise monolayer protected metal nanoclusters. Four isostructural Ag/cyanurate/phosphine metallamacrocyclic monolayer protected Ag22 nanoclusters are synthesized by kinetically controlled in-situ ligand formation-driven strategy. These eight-electron superatomic silver nanoclusters feature an unprecedented interfacial bonding structure with diverse E-Ag (E=O/N/P/Ag) interactions between the Ag13 core and metallamacrocyclic monolayer, and displays thermally activated delayed fluorescence (TADF), benefiting from their distinct donor-acceptor type electronic structures. This work not only unmasks a new core-shell interface involving cyanurate ligand but also underlines the significance of high-electron-affinity N-heterocyclic ligand in synthesizing TADF metal nanoclusters. This is the first mixed valence Ag0/I nanocluster with TADF characteristic.

Quantum Orbital Minimization Method for Excited States Calculation on a Quantum Computer.

We propose a quantum-classical hybrid variational algorithm, the quantum orbital minimization method (qOMM), for obtaining the ground state and low-lying excited states of a Hermitian operator. Given parametrized ansatz circuits representing eigenstates, qOMM implements quantum circuits to represent the objective function in the orbital minimization method and adopts a classical optimizer to minimize the objective function with respect to the parameters in ansatz circuits. The objective function has an orthogonality constraint implicitly embedded, which allows qOMM to apply a different ansatz circuit to each input reference state. We carry out numerical simulations that seek to find excited states of H2, LiH, and a toy model consisting of four hydrogen atoms arranged in a square lattice in the STO-3G basis with UCCSD ansatz circuits. Comparing the numerical results with existing excited states methods, qOMM is less prone to getting stuck in local minima and can achieve convergence with more shallow ansatz circuits.

Nuclearity enlargement from [PW9O34@Ag51] to [(PW9O34)2@Ag72] and 2D and 3D network formation driven by bipyridines.

The structural transformations of metal nanoclusters are typically quite complex processes involving the formation and breakage of several bonds, and thus are challenging to study. Herein, we report a case where two lacunary Keggin polyoxometallate templated silver single-pods [PW9O34@Ag51] (SD/Ag51b) fuse to a double-pod [(PW9O34)2@Ag72] by reacting with 4,4'-bipyridine (bipy) or 1,4-bis(4-pyridinylmethyl)piperazine (pi-bipy). Their crystal structures reveal the formation of a 2D 44-sql layer (SD/Ag72a) with bipy and a 3D pcu framework (SD/Ag72c) with pi-bipy. The PW9O349- retains its structure during the cluster fusion and cluster-based network formation. Although the two processes, stripping of an Ag-ligands interface followed by fusion, and polymerization, are difficult to envisage, electrospray ionization mass spectrometry provides enough evidences for such a proposal to be made. Through this example, we expect the structural transformation to become a powerful method for synthesizing silver nanoclusters and their infinite networks, and to evolve from trial-and-error to rational.

Facile high yield, excellent catalytic performance of polyoxometalate-based lanthanide phosphine oxide complexes: Syntheses, structures, photocatalysis and THz spectra.

Water pollution, which continuously threatens human health and the sustainable development of society, has become a major concern. Photocatalytic degradation is an effective strategy to remove organic dyes from wastewater. For this strategy, it is crucial to select the appropriate catalyst. Using triphenylphosphine oxide (OPPh3) as the ligand, phosphomolybdic acid as the anion template, three new lanthanide complexes [Ln(OPPh3)4(H2O)3](PMo12O40)∙4C2H5OH (1-3) (Ln = Sm, Gd, Tb) were synthesized. The raw materials for the reaction are cheap and readily available. The convenient synthesis method is environmentally friendly, with high yield (70%-80%). Complexes 1-3 are all seven-coordinated mononuclear structures centered on lanthanide ions, [PMo12O40]3- anions and solvent molecules are not coordinated with metal ions. These mononuclear structures eventually form complicated 3D supramolecular structures through hydrogen bonds, Mo-O … π or C-H … π weak interactions. Complexes 1-3 photocatalytic degradation of MB have high removal rates, as catalysts have enough stability to be reused, and can be used as excellent catalysts for the degradation of dye molecules in sewage. Among them, the removal rate of MB by photodegradation of complex 2 was highest (99.50%). In addition, the effects of different initial concentrations of MB solution and different types of organic dyes on the photocatalysis experiment were investigated. The photocatalytic reaction mechanism of complexes 1-3 was also studied. Due to the similar structures of complexes 1-3, they have almost the same THz absorption spectra with different absorption intensity, which may be attributed to the difference of the number of weak interactions. Therefore, terahertz spectroscopy can be used as a sensitive method to distinguish and determine small differences between lanthanide-organic complexes. This is the first time that this spectrum has been used to characterize lanthanide phosphine oxide complexes modified by [PMo12O40]3-.

Toward Controlled Syntheses of Diphosphine-Protected Homochiral Gold Nanoclusters through Precursor Engineering.

Controllable syntheses of Au nanoclusters (NCs) with different nuclearities are of great significance due to the kernel-dependent physicochemical properties. Herein, two pairs of enantiomeric Au NCs [Au19(R/S-BINAP)4(PhC≡C)Cl4] (SD/Au19) and [Au11(R/S-BINAP)4(PhC≡C)2]·Cl (SD/Au11), both with atropos (rigid axial chirality) diphosphine BINAP (2,2'-bis(diphenylphosphino)-1,1'-binaphthalene) as the predominant organic ligands, were controllably synthesized through precursor engineering. The former was obtained by direct reduction of HAuCl4·4H2O, while the latter was obtained by reduction of [Au(SMe2)Cl] instead. Intriguingly, the kernel of SD/Au19 contains an Au7 pentagonal bipyramid capped by two boat-like Au6 rings, which represents another type of Au19 kernel, making SD/Au19 a good candidate for comparative study with other Au19 NCs to get more insight into the distinct structural evolution of phosphine-protected Au NCs. Despite the previous chiroptical studies on some other chiral undecagold NCs, the successful attainment of the X-ray crystal structures for SD/Au11 not only provides a step forward toward better correlating the chiroptical activities with their structural details but also reveals that even the auxiliary protecting ligands also play a nontrivial role in tuning the geometrical structures of the metal NCs. The chiroptical activities of both SD/Au19 and SD/Au11 were found to originate from the chiral ligands and core distortions; the extended π-electron systems in the BINAP ligands have proved to positively contribute to the electronic absorptions and thus disturb the corresponding circular dichroism (CD) responses.

Revealing the chirality origin and homochirality crystallization of Ag14 nanocluster at the molecular level.

Although chirality is an ever-present characteristic in biology and some artificial molecules, controlling the chirality and demystifying the chirality origin of complex assemblies remain challenging. Herein, we report two homochiral Ag14 nanoclusters with inherent chirality originated from identical rotation of six square faces on a Ag8 cube driven by intra-cluster π···π stacking interaction between pntp- (Hpntp = p-nitrothiophenol) ligands. The spontaneous resolution of the racemic (SD/rac-Ag14a) to homochiral nanoclusters (SD/L-Ag14 and SD/R-Ag14) can be realized by re-crystallizing SD/rac-Ag14a in acetonitrile, which promotes the homochiral crystallization in solid state by forming C-H···O/N hydrogen bonds with nitro oxygen atoms in pntp- or aromatic hydrogen atoms in dpph (dpph = 1,6-bis(diphenylphosphino)hexane) on Ag14 nanocluster. This work not only provides strategic guidance for the syntheses of chiral silver nanoclusters in an all-achiral environment, but also deciphers the origin of chirality at molecular level by identifying the special effects of intra- and inter-cluster supramolecular interactions.

Recommendations for offline combustion-based nitrogen isotopic analysis of silicate minerals and rocks.

RATIONALE: Due to isotope fractionations during partial nitrogen release from minerals and rocks, the complete extraction of nitrogen for analysis is crucial to ensure high-quality nitrogen isotopic data. However, the appropriate nitrogen extraction conditions (e.g. temperature, duration) have not been established for most silicate minerals and rocks. METHODS: Nitrogen in a number of common minerals and rocks was extracted using the most robust sealed-tube offline combustion techniques, purified and quantified in a custom-made metal manifold, and carried by helium gas to an isotope ratio mass spectrometer for isotopic measurement at nanomolar nitrogen level. Each mineral or rock was combusted in a variety of temperature and duration conditions to compare the nitrogen yields and isotopic compositions. RESULTS: The nitrogen yields and isotopic compositions of minerals and rocks are strongly affected by combustion temperature and duration. The optimal combustion temperature is lowest for cyclosilicate minerals, followed by phyllosilicate, tectosilicate and inosilicate minerals. Preheating of samples can induce significant nitrogen loss and δ15 N shift. Heating of samples above their optimal temperatures may cause nitrogen re-assimilation by the residual mineral or rock. CONCLUSIONS: Each mineral or rock has a characteristic optimal temperature and duration for complete nitrogen release. Preheating, under-heating or over-heating can cause nitrogen loss and isotopic shift. Therefore, we recommend using the offline combustion techniques and the optimal combustion conditions obtained in this study for nitrogen quantification and isotopic analysis of silicate minerals and rocks.

Long non-coding antisense RNA HYOU1-AS is essential to human breast cancer development through competitive binding hnRNPA1 to promote HYOU1 expression.

Triple negative breast cancer (TNBC) has poor prognosis due to lack of biomarker and therapeutic target. Emerging research has revealed long noncoding RNAs (lncRNAs) are involved in breast cancer progression, but their functions and regulatory mechanisms remain poorly understood, especially in TNBC. In this study, we performed lncRNA microarray analysis of five TNBC samples and their matched normal tissues, and discovered a number of differentially expressed lncRNAs. We identified an antisense lncRNA, HYOU1-AS, which is transcribed from the opposite strand of the hypoxia up-regulated 1 (HYOU1) gene, enriched in the nucleus and highly expressed in TNBC. HYOU1-AS knockdown could inhibit the proliferation and migration of the TNBC MDA-MB-231 cells, and reduce their xenograft tumor formation in nude mice. In mechanistic studies, we found that HYOU1-AS could promote the expression of HYOU1, a proliferative gene, through competitively binding to hnRNPA1, an RNA-binding protein, to relieve its post-transcriptional inhibition of the HYOU1 mRNA. Consistently, increased HYOU1 levels correlated with poor clinical outcomes of breast cancer patients based on our study of the TCGA database. Overall, our data indicated that the lncRNA HYOU1-AS promoted TNBC progression through upregulating HYOU1.

Multi-Modal Chiral Superstructures in Self-Assembled Anthracene-Terminal Amino Acids with Predictable and Adjustable Chiroptical Activities and Color Evolution.

Deep understanding of structure-property relationship between packing of chiral building units and their chiroptical behaviors would significantly facilitate the rational design and fabrication of the emerging chiroptical materials such as circularly polarized luminescence (CPL) emissive materials. In this paper, we unveil the universal existence of supramolecular tilt helical superstructures in self-assembled π-conjugated amino acid derivatives. A series of coded amino acid methyl esters were conjugated to anthracene segments at N-terminus, which afforded 21 and 31 symmetry supramolecular tilt chirality in solid-states. Helical assemblies enabled diversified Cotton effects and CPL performances, which were in accordance with the tilted chirality between anthracene segments. Such correlation shows fine universality, whereby the chiroptical prediction could be realized. Furthermore, on top of charge-transfer complexation, manipulation of CPL emission colors and handedness were realized.

Optimal Orbital Selection for Full Configuration Interaction (OptOrbFCI): Pursuing the Basis Set Limit under a Budget.

Full configuration interaction (FCI) solvers are limited to small basis sets due to their expensive computational costs. An optimal orbital selection for FCI (OptOrbFCI) is proposed to boost the power of existing FCI solvers to pursue the basis set limit under a computational budget. The optimization problem coincides with that of the complete active space SCF method (CASSCF), while OptOrbFCI is algorithmically quite different. OptOrbFCI effectively finds an optimal rotation matrix via solving a constrained optimization problem directly to compress the orbitals of large basis sets to one with a manageable size, conducts FCI calculations only on rotated orbital sets, and produces a variational ground-state energy and its wave function. Coupled with coordinate descent full configuration interaction (CDFCI), we demonstrate the efficiency and accuracy of the method on the carbon dimer and nitrogen dimer under basis sets up to cc-pV5Z. We also benchmark the binding curve of the nitrogen dimer under the cc-pVQZ basis set with 28 selected orbitals, which provide consistently lower ground-state energies than the FCI results under the cc-pVDZ basis set. The dissociation energy in this case is found to be of higher accuracy.

The CECAM electronic structure library and the modular software development paradigm.

First-principles electronic structure calculations are now accessible to a very large community of users across many disciplines, thanks to many successful software packages, some of which are described in this special issue. The traditional coding paradigm for such packages is monolithic, i.e., regardless of how modular its internal structure may be, the code is built independently from others, essentially from the compiler up, possibly with the exception of linear-algebra and message-passing libraries. This model has endured and been quite successful for decades. The successful evolution of the electronic structure methodology itself, however, has resulted in an increasing complexity and an ever longer list of features expected within all software packages, which implies a growing amount of replication between different packages, not only in the initial coding but, more importantly, every time a code needs to be re-engineered to adapt to the evolution of computer hardware architecture. The Electronic Structure Library (ESL) was initiated by CECAM (the European Centre for Atomic and Molecular Calculations) to catalyze a paradigm shift away from the monolithic model and promote modularization, with the ambition to extract common tasks from electronic structure codes and redesign them as open-source libraries available to everybody. Such libraries include "heavy-duty" ones that have the potential for a high degree of parallelization and adaptation to novel hardware within them, thereby separating the sophisticated computer science aspects of performance optimization and re-engineering from the computational science done by, e.g., physicists and chemists when implementing new ideas. We envisage that this modular paradigm will improve overall coding efficiency and enable specialists (whether they be computer scientists or computational scientists) to use their skills more effectively and will lead to a more dynamic evolution of software in the community as well as lower barriers to entry for new developers. The model comes with new challenges, though. The building and compilation of a code based on many interdependent libraries (and their versions) is a much more complex task than that of a code delivered in a single self-contained package. Here, we describe the state of the ESL, the different libraries it now contains, the short- and mid-term plans for further libraries, and the way the new challenges are faced. The ESL is a community initiative into which several pre-existing codes and their developers have contributed with their software and efforts, from which several codes are already benefiting, and which remains open to the community.

Accelerating Excitation Energy Computation in Molecules and Solids within Linear-Response Time-Dependent Density Functional Theory via Interpolative Separable Density Fitting Decomposition.

We present an efficient way to compute the excitation energies in molecules and solids within linear-response time-dependent density functional theory (LR-TDDFT). Conventional methods to construct and diagonalize the LR-TDDFT Hamiltonian require ultrahigh computational cost, limiting its optoelectronic applications to small systems. Our new method is based on the interpolative separable density fitting (ISDF) decomposition combined with implicitly constructing and iteratively diagonalizing the LR-TDDFT Hamiltonian and only requires low computational cost to accelerate the LR-TDDFT calculations in the plane-wave basis sets under the periodic boundary condition. We show that this method accurately reproduces excitation energies in a fullerene (C60) molecule and bulk silicon Si64 system with significantly reduced computational cost compared to conventional direct and iterative calculations. The efficiency of this ISDF method enables us to investigate the excited-state properties of liquid water absorption on MoS2 and phosphorene by using the LR-TDDFT calculations. Our computational results show that an aqueous environment has a weak effect on low excitation energies but a strong effect on high excitation energies of 2D semiconductors for photocatalytic water splitting.

Coordinate Descent Full Configuration Interaction.

We develop an efficient algorithm, coordinate descent FCI (CDFCI), for the electronic structure ground-state calculation in the configuration interaction framework. CDFCI solves an unconstrained nonconvex optimization problem, which is a reformulation of the full configuration interaction eigenvalue problem, via an adaptive coordinate descent method with a deterministic compression strategy. CDFCI captures and updates appreciative determinants with different frequencies proportional to their importance. We show that CDFCI produces accurate variational energy for both static and dynamic correlation by benchmarking the binding curve of nitrogen dimer in the cc-pVDZ basis with 10-3 mHa accuracy. We also demonstrate the efficiency and accuracy of CDFCI for strongly correlated chromium dimer in the Ahlrichs VDZ basis and produce state-of-the-art variational energy.

A comparative study on atomically precise Au nanoclusters as catalysts for the aldehyde-alkyne-amine (A3) coupling reaction: ligand effects on the nature of the catalysis and efficiency.

Atomically precise Au13 nanoclusters stabilized by stibines catalyze the aldehyde-alkyne-amine coupling reaction more efficiently than those stabilized by thiols or phosphines. The nature of the catalytic activity is also different, and may be attributed to the weaker coordinating ability of the stibine ligands.