Scalable Quantum Monte Carlo with Direct-Product Trial Wave Functions.

The computational demand posed by applying multi-Slater determinant trials in phaseless auxiliary-field quantum Monte Carlo methods (MSD-AFQMC) is particularly significant for molecules exhibiting strong correlations. Here, we propose using direct-product wave functions as trials for MSD-AFQMC, aiming to reduce computational overhead by leveraging the compactness of multi-Slater determinant trials in direct-product form (DP-MSD). This efficiency arises when the active space can be divided into noncoupling subspaces, a condition we term "decomposable active space". By employing localized-active space self-consistent field wave functions as an example of such trials, we demonstrate our proposed approach across a range of molecular systems, each exhibiting varying degrees of complexity in their electronic structures. Our findings indicate that the compact DP-MSD trials can reduce computational costs substantially, by up to 36 times for the C2H6N4 molecule where the two double bonds between nitrogen N=N are clearly separated by a C-C single bond, while maintaining accuracy when active spaces are decomposable. In the case of larger systems such as the benzene dimer, characterized by weak coupling between the two monomers, we observed a decrease in computational cost compared to using a complete active space trial, yet we retained the same level of accuracy. However, for systems where these active subspaces strongly couple, a scenario we refer to as "strong subspace coupling", the method's accuracy decreases compared to that achieved with a complete active space approach. We anticipate that our method will be beneficial for systems with noncoupling to weakly coupling subspaces that require local multireference treatments.

Twenty Years of Auxiliary-Field Quantum Monte Carlo in Quantum Chemistry: An Overview and Assessment on Main Group Chemistry and Bond-Breaking.

In this work, we present an overview of the phaseless auxiliary-field quantum Monte Carlo (ph-AFQMC) approach from a computational quantum chemistry perspective and present a numerical assessment of its performance on main group chemistry and bond-breaking problems with a total of 1004 relative energies. While our benchmark study is somewhat limited, we make recommendations for the use of ph-AFQMC for general main-group chemistry applications. For systems where single determinant wave functions are qualitatively accurate, we expect the accuracy of ph-AFQMC in conjunction with a single-determinant trial wave function to be between that of coupled-cluster with singles and doubles (CCSD) and CCSD with perturbative triples (CCSD(T)). For these applications, ph-AFQMC should be a method of choice when canonical CCSD(T) is too expensive to run. For systems where multireference (MR) wave functions are needed for qualitative accuracy, ph-AFQMC is far more accurate than MR perturbation theory methods and competitive with MR configuration interaction (MRCI) methods. Due to the computational efficiency of ph-AFQMC compared to MRCI, we recommended ph-AFQMC as a method of choice for handling dynamic correlation in MR problems. We conclude with a discussion of important directions for future development of the ph-AFQMC approach.

Excited States of Crystalline Point Defects with Multireference Density Matrix Embedding Theory.

Accurate and affordable methods to characterize the electronic structure of solids are important for targeted materials design. Embedding-based methods provide an appealing balance in the trade-off between cost and accuracy─particularly when studying localized phenomena. Here, we use the density matrix embedding theory (DMET) algorithm to study the electronic excitations in solid-state defects with a restricted open-shell Hartree-Fock (ROHF) bath and multireference impurity solvers, specifically, complete active space self-consistent field (CASSCF) and n-electron valence state second-order perturbation theory (NEVPT2). We apply the method to investigate the electronic excitations in an oxygen vacancy (OV) on a MgO(100) surface and find absolute deviations within 0.05 eV between DMET using the CASSCF/NEVPT2 solver, denoted as CAS-DMET/NEVPT2-DMET, and the nonembedded CASSCF/NEVPT2 approach. Next, we establish the practicality of DMET by extending it to larger supercells for the OV defect and a neutral silicon vacancy in diamond where the use of nonembedded CASSCF/NEVPT2 is extremely expensive.

Parental exposures increase the vulnerability of copepod offspring to copper and a simulated marine heatwave.

Extreme temperatures from marine heatwaves (MHWs) and pollution are dominant stressors in tropical marine ecosystems. However, we know little about the role of transgenerational effects of metals and MHWs in shaping the offspring's vulnerability to these stressors. We addressed this fundamental knowledge gap by exposing the planktonic copepod Pseudodiaptomus incisus to copper (Cu: control, 15 and 60 µg L-1) under 2 temperatures (30 and a simulated marine heatwave at 34 °C) in the first generation (F1) and 16 treatments in F2: offspring from each of 4 F1 conditions (control or 15 µg Cu L-1 × 30 or 34 °C) was reared in 4 F2 conditions (control or 15 µg Cu L-1 × 30 or 34 °C). We assessed changes in copepod performance, particularly survival, adult size, grazing, and reproduction. In F1, Cu or marine heatwave (MHW) exposures reduced all fitness traits of F1; the effects were particularly strong when both stressors were present. Transgenerational effects of Cu or MHW also strongly reduced F2 performance. Direct Cu and MHW effects on the offspring were further strengthened by transgenerational effects, resulting in more substantial reductions in F2 performance when both generations were exposed to these stressors. As copepods are major food resources for corals, shrimps, or fish larvae and juveniles, strong transgenerational and direct effects of Cu and MHW can have a cascading effect on entire coastal food webs. These results highlight the importance of considering the interaction of transgenerational and direct effects of multiple stressors, particularly relevant for short-lived organisms in tropical marine ecosystems.

Recent developments in the PySCF program package.

PySCF is a Python-based general-purpose electronic structure platform that supports first-principles simulations of molecules and solids as well as accelerates the development of new methodology and complex computational workflows. This paper explains the design and philosophy behind PySCF that enables it to meet these twin objectives. With several case studies, we show how users can easily implement their own methods using PySCF as a development environment. We then summarize the capabilities of PySCF for molecular and solid-state simulations. Finally, we describe the growing ecosystem of projects that use PySCF across the domains of quantum chemistry, materials science, machine learning, and quantum information science.

Author Correction: Extreme temperature impairs growth and productivity in a common tropical marine copepod.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Periodic Electronic Structure Calculations with the Density Matrix Embedding Theory.

We developed a periodic version of density matrix embedding theory, DMET, with which it is possible to perform electronic structure calculations on periodic systems and compute the band structure of solid-state materials. Electron correlation can be captured by means of a local impurity model using various wave function methods, such as full configuration interaction, coupled cluster, and multiconfigurational methods. The method is able to describe not only the ground-state energy but also the quasiparticle band picture via the real space-momentum space implementation. We investigate the performance of periodic DMET in describing the ground-state energy as well as the electronic band structure for one-dimensional solids. Our results show that DMET is in good agreement with other many-body techniques at a cheaper computational cost. We anticipate that periodic DMET can be a promising first principle method for strongly correlated materials.

Lead-free double perovskites Cs2InCuCl6 and (CH3NH3)2InCuCl6: electronic, optical, and electrical properties.

Searching for alternatives to lead-containing metal halide perovskites, we explored the properties of indium-based inorganic double perovskites Cs2InMX6 with M = Cu, Ag, Au and X = Cl, Br, I, and of its organic-inorganic hybrid derivative MA2InCuCl6 (MA = CH3NH3+) using computation within Kohn-Sham density functional theory. Among these compounds, Cs2InCuCl6 and MA2InCuCl6 were found to be potentially promising candidates for solar cells. Calculations with different functionals provided the direct band gap of Cs2InCuCl6 between 1.05 and 1.73 eV. In contrast, MA2InCuCl6 exhibits an indirect band gap between 1.31 and 2.09 eV depending on the choice of exchange-correlation functional. Cs2InCuCl6 exhibits a much higher absorption coefficient than that calculated for c-Si and CdTe, common semiconductors for solar cells. Even MA2InCuCl6 is predicted to have a higher absorption coefficient than c-Si and CdTe across the visible spectrum despite the fact that it is an indirect band gap material. The intrinsic charge carrier mobilities for Cs2InCuCl6 along the L-Γ path are predicted to be comparable to those for MAPbI3. Finally, we carried out calculations of the band edge positions for MA2InCuCl6 and Cs2InCuCl6 to offer guidance for solar cell heterojunction design and optimization. We conclude that Cs2InCuCl6 and MA2InCuCl6 are promising semiconductors for photovoltaic and optoelectronic applications.

Extreme temperature impairs growth and productivity in a common tropical marine copepod.

Shallow, tropical marine ecosystems provide essential ecosystem goods and services, but it is unknown how these ecosystems will respond to the increased exposure to the temperature extremes that are likely to become more common as climate change progresses. To address this issue, we tracked the fitness and productivity of a key zooplankton species, the copepod Pseudodiaptomus annandalei, acclimated at two temperatures (30 and 34 °C) over three generations. 30 °C is the mean temperature in the shallow water of the coastal regions in Southeast Asia, while 34 °C simulated a temperature extreme that occurs frequently during the summer period. For each generation, we measured the size at maturity and reproductive success of individuals. In all three generations, we found strong negative effects of warming on all measured fitness-related parameters, including prolonged development time, reduced size at maturity, smaller clutch sizes, lower hatching success, and reduced naupliar production. Our results suggest that P. annandalei are already exposed to temperatures that exceed their upper thermal optimum. Increased exposure to extreme temperatures may reduce the abundance of these tropical marine copepods, and thus reduce the availability of resources to higher trophic levels.

Electron delocalization in single-layer phthalocyanine-based covalent organic frameworks: a first principle study.

In this work, we first investigate the localized electronic states in the band structures of three single-layer COFs based on typical building units of COFs chemistry. Our results confirm that the polar nature of strong bonds in these building units is a hindrance to a fully delocalized structure and disfavors the band-like mechanism of transport. We then show that a rational design of the building units can lead to dispersive band states in the electronic structure and results in conducting single-layer COFs. We demonstrate this strategy by investigating the charge carrier transport in a series of single-layer Ni-phthalocyanine (NiPc) covalent organic frameworks (COFs), namely, NiPc-P, NiPc-2P, and NiPc-3P. Three proposed COFs exhibit semiconducting band gaps ranging from 0.55 to 0.91 eV. Their room-temperature intrinsic mobility is predicted to be in range of 200-600 cm2 V-1 s-1 and 20 000-60 000 cm2 V-1 s-1 for electrons and holes, respectively, which are comparable to those of phosphorene and higher than those of the trigonal prismatic molybdenum disulfide. NiPc are dynamically and mechanically stable and can be synthesized via the co-evaporation between Ni and corresponding tetracyano linkers. Importantly, we demonstrate that the properties of the single-layer COFs can be tuned by engineering the organic building blocks. Our theoretical study not only provides insight into the design principles for semiconducting single-layer COFs but also highlights the significance of reticular chemistry in the development of a new generation of two-dimensional materials for optoelectronic applications.

Can Density Matrix Embedding Theory with the Complete Activate Space Self-Consistent Field Solver Describe Single and Double Bond Breaking in Molecular Systems?

Density matrix embedding theory (DMET) [ Phys. Rev. Lett. 2012, 109, 186404] has been demonstrated as an efficient wave-function-based embedding method to treat extended systems. Despite its success in many quantum lattice models, the extension of DMET to real chemical systems has been tested only on selected cases. Herein, we introduce the use of the complete active space self-consistent field (CASSCF) method as a correlated impurity solver for DMET, leading to a method called CAS-DMET. We test its performance in describing the dissociation of H-H single bonds in a H10 ring model system and an N═N double bond in azomethane (CH3-N═N-CH3) and pentyldiazene (CH3(CH2)4-N═NH). We find that the performance of CAS-DMET is comparable to CASSCF with different active space choices when single-embedding DMET corresponding to only one embedding problem for the system is used. When multiple embedding problems are used for the system, the CAS-DMET is in good agreement with CASSCF for the geometries around the equilibrium, but not in equal agreement at bond dissociation.

A Natural Vibrio parahaemolyticus ΔpirA Vp pirB Vp+ Mutant Kills Shrimp but Produces neither Pir Vp Toxins nor Acute Hepatopancreatic Necrosis Disease Lesions.

Acute hepatopancreatic necrosis disease (AHPND) of shrimp is caused by Vibrio parahaemolyticus isolates (VPAHPND isolates) that harbor a pVA plasmid encoding toxins PirA Vp and PirB Vp These are released from VPAHPND isolates that colonize the shrimp stomach and produce pathognomonic AHPND lesions (massive sloughing of hepatopancreatic tubule epithelial cells). PCR results indicated that V. parahaemolyticus isolate XN87 lacked pirA Vp but carried pirB Vp Unexpectedly, Western blot analysis of proteins from the culture broth of XN87 revealed the absence of both toxins, and the lack of PirB Vp was further confirmed by enzyme-linked immunosorbent assay. However, shrimp immersion challenge with XN87 resulted in 47% mortality without AHPND lesions. Instead, lesions consisted of collapsed hepatopancreatic tubule epithelia. In contrast, control shrimp challenged with typical VPAHPND isolate 5HP gave 90% mortality, accompanied by AHPND lesions. Sequence analysis revealed that the pVA plasmid of XN87 contained a mutated pirA Vp gene interrupted by the out-of-frame insertion of a transposon gene fragment. The upstream region and the beginning of the original pirA Vp gene remained intact, but the insertion caused a 2-base reading frameshift in the remainder of the pirA Vp gene sequence and in the downstream pirB Vp gene sequence. Reverse transcription-PCR and sequencing of 5HP revealed a bicistronic pirAB Vp mRNA transcript that was not produced by XN87, explaining the absence of both toxins in its culture broth. However, the virulence of XN87 revealed that some V. parahaemolyticus isolates carrying mutant pVA plasmids that produce no Pir Vp toxins can cause mortality in shrimp in ponds experiencing an outbreak of early mortality syndrome (EMS) but may not have been previously recognized to be AHPND related because they did not cause pathognomonic AHPND lesions.IMPORTANCE Shrimp acute hepatopancreatic necrosis disease (AHPND) is caused by Vibrio parahaemolyticus isolates (VPAHPND isolates) that harbor the pVA1 plasmid encoding toxins PirA Vp and PirB Vp The toxins are produced in the shrimp stomach but cause death by massive sloughing of hepatopancreatic tubule epithelial cells (pathognomonic AHPND lesions). V. parahaemolyticus isolate XN87 harbors a mutant pVA plasmid that produces no Pir toxins and does not cause AHPND lesions but still causes ∼50% shrimp mortality. Such isolates may cause a portion of the mortality in ponds experiencing an outbreak of EMS that is not ascribed to VPAHPND Thus, they pose to shrimp farmers an additional threat that would be missed by current testing for VPAHPND Moribund shrimp from ponds experiencing an outbreak of EMS that exhibit collapsed hepatopancreatic tubule epithelial cells can serve as indicators for the possible presence of such isolates, which can then be confirmed by additional PCR tests for the presence of a pVA plasmid.

Synthesis and Selective CO2 Capture Properties of a Series of Hexatopic Linker-Based Metal-Organic Frameworks.

Four crystalline, porous metal-organic frameworks (MOFs), based on a new hexatopic linker, 1',2',3',4',5',6'-hexakis(4-carboxyphenyl)benzene (H6CPB), were synthesized and fully characterized. Interestingly, two members of this series exhibited new topologies, namely, htp and hhp, which were previously unseen in MOF chemistry. Gas adsorption measurements revealed that all members exhibited high CO2 selectivity over N2 and CH4. Accordingly, breakthrough measurements were performed on a representative example, in which the effective separation of CO2 from binary mixtures containing either N2 or CH4 was demonstrated without any loss in performance over three consecutive cycles.

Tailoring the Optical Absorption of Water-Stable Zr(IV)- and Hf(IV)-Based Metal-Organic Framework Photocatalysts.

New Zr(IV)- and Hf(IV)-based metal-organic framework photocatalysts, termed VNU-1 and VNU-2 (where VNU = Vietnam National University), were synthesized and their resulting structures fully characterized. By employing a highly π-conjugated linker, namely 1,4-bis(2-[4-carboxyphenyl]ethynyl)benzene, the optical absorption properties were effectively red-shifted into the visible light region. This strategy, coupled with the high water stability of the materials, led to enhanced MOF-driven photocatalytic degradation, under ultraviolet-visible light, of organic dye pollutants commonly found in wastewater.