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"Free energy"
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Guidelines for the analysis of free energy calculations
Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool,
alchemical-analysis.py
, freely available on GitHub as part of the pymbar package (located at
http://github.com/choderalab/pymbar
), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.
Journal Article
FreeSolv: a database of experimental and calculated hydration free energies, with input files
This work provides a curated database of experimental and calculated hydration free energies for small neutral molecules in water, along with molecular structures, input files, references, and annotations. We call this the Free Solvation Database, or FreeSolv. Experimental values were taken from prior literature and will continue to be curated, with updated experimental references and data added as they become available. Calculated values are based on alchemical free energy calculations using molecular dynamics simulations. These used the GAFF small molecule force field in TIP3P water with AM1-BCC charges. Values were calculated with the GROMACS simulation package, with full details given in references cited within the database itself. This database builds in part on a previous, 504-molecule database containing similar information. However, additional curation of both experimental data and calculated values has been done here, and the total number of molecules is now up to 643. Additional information is now included in the database, such as SMILES strings, PubChem compound IDs, accurate reference DOIs, and others. One version of the database is provided in the Supporting Information of this article, but as ongoing updates are envisioned, the database is now versioned and hosted online. In addition to providing the database, this work describes its construction process. The database is available free-of-charge via
http://www.escholarship.org/uc/item/6sd403pz
.
Journal Article
Tailoring grain boundary stability of zinc-titanium alloy for long-lasting aqueous zinc batteries
The detrimental parasitic reactions and uncontrolled deposition behavior derived from inherently unstable interface have largely impeded the practical application of aqueous zinc batteries. So far, tremendous efforts have been devoted to tailoring interfaces, while stabilization of grain boundaries has received less attention. Here, we demonstrate that preferential distribution of intermetallic compounds at grain boundaries via an alloying strategy can substantially suppress intergranular corrosion. In-depth morphology analysis reveals their thermodynamic stability, ensuring sustainable potency. Furthermore, the hybrid nucleation and growth mode resulting from reduced Gibbs free energy contributes to the spatially uniform distribution of Zn nuclei, promoting the dense Zn deposition. These integrated merits enable a high Zn reversibility of 99.85% for over 4000 cycles, steady charge-discharge at 10 mA cm
−2
, and impressive cyclability for roughly 3500 cycles in Zn-Ti//NH
4
V
4
O
10
full cell. Notably, the multi-layer pouch cell of 34 mAh maintains stable cycling for 500 cycles. This work highlights a fundamental understanding of microstructure and motivates the precise tuning of grain boundary characteristics to achieve highly reversible Zn anodes.
The electrochemical performance of metal electrodes is significantly influenced by their grain boundary stability. Here, the authors propose a zinc-titanium two-phase alloy via grain boundary engineering to inhibit intergranular corrosion and tailor deposition behavior for stable aqueous zinc batteries.
Journal Article
Nano-metal diborides-supported anode catalyst with strongly coupled TaOx/IrO2 catalytic layer for low-iridium-loading proton exchange membrane electrolyzer
The sluggish kinetics of oxygen evolution reaction (OER) and high iridium loading in catalyst coated membrane (CCM) are the key challenges for practical proton exchange membrane water electrolyzer (PEMWE). Herein, we demonstrate high-surface-area nano-metal diborides as promising supports of iridium-based OER nanocatalysts for realizing efficient, low-iridium-loading PEMWE. Nano-metal diborides are prepared by a novel disulphide-to-diboride transition route, in which the entropy contribution to the Gibbs free energy by generation of gaseous sulfur-containing products plays a crucial role. The nano-metal diborides, TaB
2
in particular, are investigated as the support of IrO
2
nanocatalysts, which finally forms a TaO
x
/IrO
2
heterojunction catalytic layer on TaB
2
surface. Multiple advantageous properties are achieved simultaneously by the resulting composite material (denoted as IrO
2
@TaB
2
), including high electrical conductivity, improved iridium mass activity and enhanced corrosion resistance. As a consequence, the IrO
2
@TaB
2
can be used to fabricate the membrane electrode with a low iridium loading of 0.15 mg cm
−2
, and to give an excellent catalytic performance (3.06 A cm
−2
@2.0 V@80
o
C) in PEMWE―the one that is usually inaccessible by unsupported Ir-based nanocatalysts and the vast majority of existing supported Ir-based catalysts at such a low iridium loading.
The extreme scarcity of Ir largely limits the wide application of proton exchange membrane water electrolyzer (PEMWE) for hydrogen production. Here, the authors report high-surface area nano-metal diboride as promising support of anode nanocatalyst IrO
2
for realizing efficient, low Ir loading PEMWE.
Journal Article
Dual donor-acceptor covalent organic frameworks for hydrogen peroxide photosynthesis
Constructing photocatalytically active and stable covalent organic frameworks containing both oxidative and reductive reaction centers remain a challenge. In this study, benzotrithiophene-based covalent organic frameworks with spatially separated redox centers are rationally designed for the photocatalytic production of hydrogen peroxide from water and oxygen without sacrificial agents. The triazine-containing framework demonstrates high selectivity for H
2
O
2
photogeneration, with a yield rate of 2111 μM h
−1
(21.11 μmol h
−1
and 1407 μmol g
−1
h
−1
) and a solar-to-chemical conversion efficiency of 0.296%. Codirectional charge transfer and large energetic differences between linkages and linkers are verified in the double donor-acceptor structures of periodic frameworks. The active sites are mainly concentrated on the electron-acceptor fragments near the imine bond, which regulate the electron distribution of adjacent carbon atoms to optimally reduce the Gibbs free energy of O
2
* and OOH* intermediates during the formation of H
2
O
2
.
In this study, benzotrithiophene-based covalent organic frameworks with spatially separated oxidative and reductive reaction centers are rationally designed for photocatalytic production of H
2
O
2
from water and oxygen without sacrificial agents.
Journal Article
Cation-driven phase transition and anion-enhanced kinetics for high energy efficiency zinc-interhalide complex batteries
Aqueous Zn-halogen batteries, valued for high safety, large capacity, and low cost, suffer from the polyhalide shuttle effect and chaotic zinc electrodeposition, reducing energy efficiency and lifespan. Here we show a cation-driven positive electrode phase transition to suppress the shuttle effect and achieve uniform zinc electrodeposition, along with an anion kinetic enhancement strategy to improve energy efficiency and lifespan. Taking tetramethylammonium halide (TMAX, X = F, Cl, Br) as a subject, TMA
+
promotes oriented zinc (101) deposition on the negative electrode through electrostatic shielding, significantly extending cycling life. Concurrently, it captures I
3
–
on the positive electrode, forming a stable solid-phase interhalide complex that enhances coulombic efficiency. Compared to I
3
–
and TMAI
3
, X
–
anions lower the Gibbs free energy differences of I
–
→ I
2
X
–
and I
2
X
–
→ TMAI
2
X, accelerating I
–
/I
2
X
–
/TMAI
2
X conversions and improving voltage efficiency. In TMAF-modified electrolytes, zinc interhalide complex batteries achieve a high energy efficiency of 95.2% at 0.2 A g
–1
with good reversibility, showing only 0.1% capacity decay per cycle over 1000 cycles. At 1 A g
–1
, they show a low decay rate of 0.1‰ per cycle across 10,000 cycles. This study provides insights into enhancing energy efficiency and long-term stability for sustainable energy storage.
Aqueous Zn-halogen batteries suffer from efficiency loss due to polyhalide shuttling and chaotic Zn plating. Here, authors demonstrate a cation-anion synergy strategy that suppresses shuttling and directs uniform Zn deposition, achieving 95.2% high energy efficiency.
Journal Article
Adaptive Monte Carlo augmented with normalizing flows
Many problems in the physical sciences, machine learning, and statistical inference necessitate sampling from a high-dimensional, multimodal probability distribution. Markov Chain Monte Carlo (MCMC) algorithms, the ubiquitous tool for this task, typically rely on random local updates to propagate configurations of a given system in a way that ensures that generated configurations will be distributed according to a target probability distribution asymptotically. In high-dimensional settings with multiple relevant metastable basins, local approaches require either immense computational effort or intricately designed importance sampling strategies to capture information about, for example, the relative populations of such basins. Here, we analyze an adaptive MCMC, which augments MCMC sampling with nonlocal transition kernels parameterized with generative models known as normalizing flows. We focus on a setting where there are no preexisting data, as is commonly the case for problems in which MCMC is used. Our method uses 1) an MCMC strategy that blends local moves obtained from any standard transition kernel with those from a generative model to accelerate the sampling and 2) the data generated this way to adapt the generative model and improve its efficacy in the MCMC algorithm. We provide a theoretical analysis of the convergence properties of this algorithm and investigate numerically its efficiency, in particular in terms of its propensity to equilibrate fast between metastable modes whose rough location is known a priori but respective probability weight is not. We show that our algorithm can sample effectively across large free energy barriers, providing dramatic accelerations relative to traditional MCMC algorithms.
Journal Article
Perovskite heteroepitaxy for high-efficiency and stable pure-red LEDs
Ultrasmall CsPbI
3
perovskite quantum dots (QDs) are the most promising candidates for realizing efficient and stable pure-red perovskite light-emitting diodes (PeLEDs)
1
,
2
,
3
,
4
–
5
. However, it is challenging for ultrasmall CsPbI
3
QDs to retain their solution-phase properties when they assemble into conductive films, greatly hindering their device application
3
,
6
. Here we report an approach for in situ deposit stabilized ultrasmall CsPbI
3
QD conductive solids, by constructing CsPbI
3
QD/quasi
-
two-dimensional (quasi-2D) perovskite heteroepitaxy. The well-aligned periodic array of edge-oriented ligands at heterointerface triggers a substantial octahedral tilting in a critical layer thickness of CsPbI
3
QDs, which heightens the Gibbs free energy difference between the tilted-CsPbI
3
and δ-CsPbI
3
leading to thermodynamic stabilization of CsPbI
3
QDs. The approach allows us to fabricate stabilized CsPbI
3
QD conductive films with tunable emission covering the entire red spectral region from 600 nm to 710 nm. Here we report the pure-red PeLEDs with narrow electroluminescence peak centred at 630 nm, matching the Rec. 2100 standard for ultrahigh-definition display. The champion device exhibits a certified external quantum efficiency of 24.6% and a half-lifetime of 6,330 min, ranking as one of the most efficient and stable pure-red PeLED reported to date. The approach is also compatible with large-area manufacturing, enabling 1 cm
2
PeLED to exhibit the best external quantum efficiency of 20.5% at 630 nm.
A heteroepitaxial-strain-based strategy for enhancing the stability of perovskite quantum dots for spectrally narrow (pure) red LEDs is reported.
Journal Article
Stabilized Cu0 -Cu1+ dual sites in a cyanamide framework for selective CO2 electroreduction to ethylene
Electrochemical reduction of carbon dioxide to produce high-value ethylene is often limited by poor selectivity and yield of multi-carbon products. To address this, we propose a cyanamide-coordinated isolated copper framework with both metallic copper (Cu
0
) and charged copper (Cu
1+
) sites as an efficient electrocatalyst for the reduction of carbon dioxide to ethylene. Our
operando
electrochemical characterizations and theoretical calculations reveal that copper atoms in the Cu
δ+
NCN complex enhance carbon dioxide activation by improving surface carbon monoxide adsorption, while delocalized electrons around copper sites facilitate carbon-carbon coupling by reducing the Gibbs free energy for *CHC formation. This leads to high selectivity for ethylene production. The Cu
δ+
NCN catalyst achieves 77.7% selectivity for carbon dioxide to ethylene conversion at a partial current density of 400 milliamperes per square centimeter and demonstrates long-term stability over 80 hours in membrane electrode assembly-based electrolysers. This study provides a strategic approach for designing catalysts for the electrosynthesis of value-added chemicals from carbon dioxide.
This study reports a cyanamide-framework stabilized multivalent copper catalyst for efficient electrochemical reduction of carbon dioxide to ethylene with 77.7% selectivity at 400 mA cm
−2
, offering a rational strategy for CO
2
conversion.
Journal Article