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| Open AccessData-driven design of molecular nanomagnets
Three decades of research in molecular nanomagnets have enabled the preparation of compounds displaying magnetic memory at liquid nitrogen temperature. Here, the authors provide an innovative framework for the design of molecular magnets based on data mining, and develop an interactive dashboard to visualize the dataset.
- Yan Duan
- , Lorena E. Rosaleny
- & Alejandro Gaita-Ariño
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Article
| Open AccessObservation of a transient intermediate in the ultrafast relaxation dynamics of the excess electron in strong-field-ionized liquid water
A unified picture of the electronic relaxation dynamics of ionized liquid water remains elusive despite decades of study. Here, the authors use few-cycle optical pump-probe spectroscopy and ab initio quantum dynamics to unambiguously identify a new transient intermediate in the relaxation pathway.
- Pei Jiang Low
- , Weibin Chu
- & Zhi-Heng Loh
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| Open AccessHow mono- and diphosphine ligands alter regioselectivity of the Rh-catalyzed annulative cleavage of bicyclo[1.1.0]butanes
Ligands alter the regioselectivity of Rh(I)- catalyzed cycloisomerizations of bicyclobutanes. Here, mechanistic studies performed by the authors pinpoint a concerted C−C bond cleavage and carbenoid formation responsible for the divergence.
- Pan-Pan Chen
- , Peter Wipf
- & K. N. Houk
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Article
| Open AccessPath sampling of recurrent neural networks by incorporating known physics
Adding prior experimentally or theoretically obtained knowledge to the training of recurrent neural networks may be challenging due to their feedback nature with arbitrarily long memories. The authors propose a path sampling approach that allows to include generic thermodynamic or kinetic constraints for learning of time series relevant to molecular dynamics and quantum systems.
- Sun-Ting Tsai
- , Eric Fields
- & Pratyush Tiwary
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| Open AccessA theory-driven synthesis of symmetric and unsymmetric 1,2-bis(diphenylphosphino)ethane analogues via radical difunctionalization of ethylene
DPPEs are fundamental bidentate ligands with a C2-alkyl-linker chain for many transition-metal-catalyzed reactions. Here, authors utilize the AFIR method to develop a practical synthetic method for both symmetric and unsymmetric DPPEs with ethylene.
- Hideaki Takano
- , Hitomi Katsuyama
- & Tsuyoshi Mita
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Article
| Open AccessCharge-separation driven mechanism via acylium ion intermediate migration during catalytic carbonylation in mordenite zeolite
The tremendous application of carbonylation reaction requires the elaborate explanation to reaction mechanism. Here the authors propose a charge-separation driven mechanism of methyl acetate formation via acylium ion intermediate in mordenite zeolite by an integrated reaction/diffusion kinetics model during the dimethyl ether carbonylation.
- Wei Chen
- , Karolina A. Tarach
- & Anmin Zheng
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Article
| Open AccessMachine learning the Hohenberg-Kohn map for molecular excited states
Density functional theory provides a formal map from the electron density to all observables of interest of a many-body system; however, maps for electronic excited states are unknown. Here, the authors demonstrate a data-driven machine learning approach for constructing multistate functionals.
- Yuanming Bai
- , Leslie Vogt-Maranto
- & William J. Glover
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Article
| Open AccessAdsorption energies on transition metal surfaces: towards an accurate and balanced description
Accurately computed chemisorption energies are essential for modeling catalytic conversions in heterogeneous catalysis, but are challenging to obtain. Here authors combine two approaches to improve this situation: standard DFT applied to the extended system, and small cluster models that can be treated with higher-level computational techniques to improve the description of chemical bonding.
- Rafael B. Araujo
- , Gabriel L. S. Rodrigues
- & Lars G. M. Pettersson
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Article
| Open AccessRetinal chromophore charge delocalization and confinement explain the extreme photophysics of Neorhodopsin
Fluorescent proteins that self-assemble and localize in the neuron membrane are vital in neurosciences, particularly in optogenetics applications. Here the authors present a quantum-mechanics/molecular mechanics model for the photoisomerization of the natural highly fluorescent Neorhodopsin, explaining the highly fluorescent quantum yield that could lead to effective visualization of neural signals.
- Riccardo Palombo
- , Leonardo Barneschi
- & Massimo Olivucci
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| Open AccessOn the fluorescence enhancement of arch neuronal optogenetic reporters
Arch-3 rhodopsin variants are common fluorescent reporters of neuronal activity. Here, the authors show with quantum chemical modelling that a set of these proteins reveals a direct proportionality between their observed fluorescence intensity and the stability of an exotic excited-state diradical intermediate.
- Leonardo Barneschi
- , Emanuele Marsili
- & Massimo Olivucci
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Article
| Open AccessThe coupling of the hydrated proton to its first solvation shell
The Zundel [H(H2O)2]+ and Eigen [H(H2O)4]+ cations exhibit radicallly different infrared spectra and are the limiting dynamical structures involved in proton mobility in liquid water. Here, the authors find through quantum dynamics simulations that two polarized water molecules and a proton suffice to explain the key spectroscopic features connected to proton mobility for both species.
- Markus Schröder
- , Fabien Gatti
- & Oriol Vendrell
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Article
| Open AccessTowards fully ab initio simulation of atmospheric aerosol nucleation
Atmosphere aerosol nucleation contributes to climate change, air pollution, and human health, however the mechanisms are complex and elusive. Here the authors propose a general workflow based on deep neural network-based force field, paving the way towards fully ab initio simulation of atmospheric aerosol nucleation.
- Shuai Jiang
- , Yi-Rong Liu
- & Wei Huang
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Article
| Open AccessNanoconfinement facilitates reactions of carbon dioxide in supercritical water
Aqueous CO2 under nanoconfinement is of great importance to the carbon storage and transport in Earth. Here, the authors apply ab initio molecular dynamics simulations to study the effects of confinement and interfaces, and show that that CO(aq) reacts more in nanoconfinement than in bulk.
- Nore Stolte
- , Rui Hou
- & Ding Pan
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Article
| Open AccessSub-optical-cycle light-matter energy transfer in molecular vibrational spectroscopy
Energy transfer between the electromagnetic field and atoms or molecules is fundamentally interesting. Here the authors demonstrate stepwise energy transfer between broadband mid-infrared optical pulses and vibrating methylsulfonylmethane molecules in aqueous solution.
- Martin T. Peschel
- , Maximilian Högner
- & Ioachim Pupeza
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Article
| Open AccessA unifying mechanism for cation effect modulating C1 and C2 productions from CO2 electroreduction
CO2 reduction rate shows a strong dependence on alkali metal cation identity but a unified molecular picture for underlying mechanism requires further investigation. Using advanced molecular simulations and experimental kinetic studies, here the authors establish a unified mechanism for cation-coupled electron transfer.
- Seung-Jae Shin
- , Hansol Choi
- & Chang Hyuck Choi
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Article
| Open AccessMechanism of C-N bonds formation in electrocatalytic urea production revealed by ab initio molecular dynamics simulation
Urea electrosyntehsis from CO2 and NOx is a challenging reaction that is becoming increasingly important. This work uses ab initio molecular dynamics simulations to reveal the origin of C-N coupling mechanisms and reaction networks in urea synthesis.
- Xin Liu
- , Yan Jiao
- & Shi-Zhang Qiao
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Article
| Open AccessActive learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt
Uncertainty-aware machine learning models are used to automate the training of reactive force fields. The method is used here to simulate hydrogen turnover on a platinum surface with unprecedented accuracy.
- Jonathan Vandermause
- , Yu Xie
- & Boris Kozinsky
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| Open AccessDeep reaction network exploration at a heterogeneous catalytic interface
This study demonstrates how reaction network characterization can be performed on heterogeneous catalytic surfaces predictively, rather than retrospectively, using automated exploration algorithms on an ethylene oligomerization exemplar reaction.
- Qiyuan Zhao
- , Yinan Xu
- & Brett M. Savoie
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Article
| Open AccessN-Heterocyclic carbene-based C-centered Au(I)-Ag(I) clusters with intense phosphorescence and organelle-selective translocation in cells
Photoluminescent gold clusters have unique chemical and physical properties based on their perturbed electronic structures. Here, the authors report the synthesis of carbon-centered Au(I)-Ag(I) clusters with high phosphorescence quantum yields using N-heterocyclic carbene ligands.
- Zhen Lei
- , Mizuki Endo
- & Mitsuhiko Shionoya
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Article
| Open AccessPhotochemical spin-state control of binding configuration for tailoring organic color center emission in carbon nanotubes
Chemical functionalization of the sidewalls of single-wall carbon nanotubes (SWCNTs) is an emerging route to introduce fluorescent quantum defects and tailor the emission properties. Here, authors demonstrate that spin-selective photochemistry diversifies SWCNT emission tunability by controlling the morphology of the emitting sites.
- Yu Zheng
- , Yulun Han
- & Sergei Tretiak
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Article
| Open AccessUnexpected steric hindrance failure in the gas phase F− + (CH3)3CI SN2 reaction
Base-induced elimination (E2) and bimolecular nucleophilic substitution (SN2) are of significant importance in physical organic chemistry. Here, the authors show that the competing factor of E2 as opposed to steric hindrance determines the low reactivity of SN2 in the F− + (CH3)3CI reaction.
- Xiaoxiao Lu
- , Chenyao Shang
- & Dong H. Zhang
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Article
| Open AccessPhotochemical and thermochemical pathways to S2 and polysulfur formation in the atmosphere of Venus
Polysulfur compounds have been ascribed as the unknown near-UV absorbers in Venusian atmosphere and play a key role in the sulfur chemical cycle of this planet. Here, authors establish their production from (SO)2 on the grounds of quantifications of photochemical and thermal pathways involved in the sulfur chemical cycle of the planet.
- Antonio Francés-Monerris
- , Javier Carmona-García
- & Daniel Roca-Sanjuán
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Article
| Open AccessSpectral signatures of excess-proton waiting and transfer-path dynamics in aqueous hydrochloric acid solutions
The spectroscopic signatures of excess protons in HCl solutions are studied by ab initio simulations and THz experiments. Two contributions beyond the normal-mode scenario are identified that reflect proton-waiting and proton-transfer processes.
- Florian N. Brünig
- , Manuel Rammler
- & Roland R. Netz
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| Open AccessEnergy-efficient pathway for selectively exciting solute molecules to high vibrational states via solvent vibration-polariton pumping
Hybrid light-matter states formed in the strong light-matter coupling regime can alter the molecular ground-state reactivity. Here, Li et al. computationally demonstrate that pumping a collection of solvent molecules forming hybrid vibrational light-matter states in an optical cavity can excite solute molecules to very high excited states.
- Tao E. Li
- , Abraham Nitzan
- & Joseph E. Subotnik
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Article
| Open AccessContrasting behaviour under pressure reveals the reasons for pyramidalization in tris(amido)uranium(III) and tris(arylthiolate) uranium(III) molecules
The reasons for which many low-coordinate complexes exhibit bent geometry, rather than a higher symmetry, are still under debate. Here, the authors use high-pressure crystallography to examine whether low-coordinate f-block molecules become more planar or pyramidal under pressure; which happens is dictated by the dipole moment of the complex and the volume of the planar form.
- Amy N. Price
- , Victoria Berryman
- & Polly L. Arnold
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Article
| Open Access3D and 2D aromatic units behave like oil and water in the case of benzocarborane derivatives
2D/2D fusion of aromatic halves leading to a global aromatic is found in many polycyclic aromatic hydrocarbons, whereas 2D/3D aromaticity is difficult to achieve. Here the authors report a computational chemistry investigation showing that 3D/2D aromatic combination is not possible.
- Jordi Poater
- , Clara Viñas
- & Francesc Teixidor
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Article
| Open AccessStability of high-temperature salty ice suggests electrolyte permeability in water-rich exoplanet icy mantles
Hot cubic ice is shown to retain dissolved salt in its lattice, suggesting the mantle of water-rich exoplanets is more permeable to electrolytes than assumed, which has implications on its properties and on the element cycles inside such planets.
- Jean-Alexis Hernandez
- , Razvan Caracas
- & Stéphane Labrosse
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| Open AccessExcited state non-adiabatic dynamics of large photoswitchable molecules using a chemically transferable machine learning potential
The authors introduce a diabatic neural network to accelerate excitedstate, non-adiabatic simulations of azobenzene derivatives. The model predicts quantum yields for unseen species that are correlated with experiment.
- Simon Axelrod
- , Eugene Shakhnovich
- & Rafael Gómez-Bombarelli
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Article
| Open AccessAccelerating amorphous polymer electrolyte screening by learning to reduce errors in molecular dynamics simulated properties
Screening polymer electrolytes for batteries is extremely expensive due to the complex structures and slow dynamics. Here the authors develop a machine learning scheme to accelerate the screening and explore a space much larger than past studies.
- Tian Xie
- , Arthur France-Lanord
- & Jeffrey C. Grossman
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Article
| Open AccessThe role of references and the elusive nature of the chemical bond
The theory of chemical bonding relies on arbitrary references. Here the authors report a fundamental study on the chemical bond showing that considering the binding fragments as objects in real space enables to eliminate inherent biases.
- Ángel Martín Pendás
- & Evelio Francisco
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Article
| Open AccessAllotropy in ultra high strength materials
Here the authors propose a crystal thermodynamics framework describing the tensor stress induced phase transformations in solids based on nonlinear elasticity and first principles calculations. The proposed approach enables balanced design of high-strength, high-ductility materials.
- A. S. L. Subrahmanyam Pattamatta
- & David J. Srolovitz
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| Open AccessLanguage models can learn complex molecular distributions
Generative models for the novo molecular design attract enormous interest for exploring the chemical space. Here the authors investigate the application of chemical language models to challenging modeling tasks demonstrating their capability of learning complex molecular distributions.
- Daniel Flam-Shepherd
- , Kevin Zhu
- & Alán Aspuru-Guzik
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| Open AccessMachine learning the metastable phase diagram of covalently bonded carbon
Exploration of metastable phases of a given elemental composition is a data-intensive task. Here the authors integrate first-principles atomistic simulations with machine learning and high-performance computing to allow a rapid exploration of the metastable phases of carbon.
- Srilok Srinivasan
- , Rohit Batra
- & Subramanian K.R.S. Sankaranarayanan
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| Open AccessReliable crystal structure predictions from first principles
Developing theoretical frameworks to predict new polymorphs is highly desirable. Here the authors present an ab initio based force-field approach for crystal structure prediction offering a dramatic computational speed-up over fully ab initio schemes.
- Rahul Nikhar
- & Krzysztof Szalewicz
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| Open AccessTowards universal neural network potential for material discovery applicable to arbitrary combination of 45 elements
Existing neural network potentials are generally designed for narrow target materials. Here the authors develop a neural network potential which is able to handle any combination of 45 elements and show its applicability in multiple domains.
- So Takamoto
- , Chikashi Shinagawa
- & Takeshi Ibuka
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| Open AccessAssessing the stability of Pd-exchanged sites in zeolites with the aid of a high throughput quantum chemistry workflow
The identification of active sites in cation exchanged-zeolites is computationally highly demanding. Here the authors employ a DFT-based computational framework to identify the energetically most favorable adsorption sites in any zeolite using a systematic high-throughput approach.
- Hassan A. Aljama
- , Martin Head-Gordon
- & Alexis T. Bell
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Article
| Open AccessRhodium-catalyzed selective direct arylation of phosphines with aryl bromides
The widespread use of biaryl monophosphines is frequently hampered by the challenges associated with their modular preparation. Here, the authors report a protocol that appends arenes to arylphosphines to access a series of these compounds via rhodium-catalysed P(III)- directed ortho C–H activation, enabling one-fold, two-fold, and threefold direct arylation.
- Dingyi Wang
- , Mingjie Li
- & Zhuangzhi Shi
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Article
| Open AccessExact simulation of pigment-protein complexes unveils vibronic renormalization of electronic parameters in ultrafast spectroscopy
Multimode vibronic mixing in model photosynthetic systems revealed by numerically exact simulations is shown to strongly modify linear and non-linear optical responses and facilitate the persistence of coherent dynamics.
- F. Caycedo-Soler
- , A. Mattioni
- & M. B. Plenio
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Article
| Open AccessZeolite-confined subnanometric PtSn mimicking mortise-and-tenon joinery for catalytic propane dehydrogenation
The atomic structure of heterogeneous catalysts is usually a blackbox. Here the authors demonstrate large-scale machine learning atomic simulations help to resolve the catalyst structure and reaction mechanism of encapsulated PtSnOx clusters in zeolite that feature a mortise-and-tenon joinery structure and the superior activity towards propane dehydrogenation.
- Sicong Ma
- & Zhi-Pan Liu
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Article
| Open AccessNano-crumples induced Sn-Bi bimetallic interface pattern with moderate electron bank for highly efficient CO2 electroreduction
It is of high interests to design catalysts for CO2 electroreduction with enhanced selectivity and activity. Here, the authors report Sn-Bi bimetallic interface-rich material with enhanced performance for CO2 reduction to formate comparing to that of Sn-Bi bulk alloy.
- Bohua Ren
- , Guobin Wen
- & Zhongwei Chen
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Article
| Open AccessE(3)-equivariant graph neural networks for data-efficient and accurate interatomic potentials
An E(3)-equivariant deep learning interatomic potential is introduced for accelerating molecular dynamics simulations. The method obtains state-of-the-art accuracy, can faithfully describe dynamics of complex systems with remarkable sample efficiency.
- Simon Batzner
- , Albert Musaelian
- & Boris Kozinsky
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Article
| Open AccessUnderstanding the rheology of nanocontacts
The rigidity of solid nanocontacts formed when metals touch is apparently lost liquidlike under large mechanical oscillations. As we show theoretically, there is no melting but oscillated nanocontacts undergo a remarkable reversible stick-slip rheology.
- Ali Khosravi
- , Antoine Lainé
- & Erio Tosatti
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Article
| Open AccessA spin promotion effect in catalytic ammonia synthesis
Catalytic ammonia synthesis continues to attract significant interest. Here, the authors develop a model to explain a large body of recent experimental data on new promoters. They find new promotion mechanism mediated by coupling between adsorption and spin polarization on the surface atoms of magnetic catalysts.
- Ang Cao
- , Vanessa J. Bukas
- & Jens K. Nørskov
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Article
| Open AccessBreaking adsorption-energy scaling limitations of electrocatalytic nitrate reduction on intermetallic CuPd nanocubes by machine-learned insights
Machine learning is a powerful tool for screening electrocatalytic materials. Here, the authors reported a seamless integration of machine-learned physical insights with the controlled synthesis of structurally ordered intermetallic nanocrystals and well-defined catalytic sites for efficient nitrate reduction to ammonia.
- Qiang Gao
- , Hemanth Somarajan Pillai
- & Huiyuan Zhu
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Article
| Open AccessAutomated exploitation of the big configuration space of large adsorbates on transition metals reveals chemistry feasibility
The discovery of heterogeneous catalysts for large molecule conversion has been lagging due to the combinatorial inventory of intermediates. Here, the author presents an automated framework to explore the chemical space of reaction intermediates.
- Geun Ho Gu
- , Miriam Lee
- & Dionisios G. Vlachos
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| Open AccessSimulating a chemically fueled molecular motor with nonequilibrium molecular dynamics
Molecular motors move in response to an imbalance between concentrations of fuel and waste molecules. Here, the authors simulate such non-equilibrium conditions to characterize a model motor’s performance and mechanism of operation.
- Alex Albaugh
- & Todd R. Gingrich
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Article
| Open AccessMolecular communications in complex systems of dynamic supramolecular polymers
The dynamic structure of supramolecular polymers is challenging to determine both in experiments and in simulations. Here the authors use coarse-grained molecular models to provide a comprehensive analysis of the molecular communication in these complex molecular systems.
- Martina Crippa
- , Claudio Perego
- & Giovanni M. Pavan
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| Open AccessChiral photochemistry of achiral molecules
The authors report non-adiabatic first principles molecular dynamics to show how an achiral molecule can be converted to a chiral one upon photoexcitation. These results demonstrate the possibility of asymmetric photochemistry starting from achiral reactants.
- Umberto Raucci
- , Hayley Weir
- & Todd J. Martínez
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Article
| Open AccessThe stability of covalent dative bond significantly increases with increasing solvent polarity
Non covalent complexes are often considerably destabilized in the solvent. Here the authors combine vibrational Raman and NMR spectroscopy with a coupled-cluster computational investigation to show that the solvent polarity enhance the complex stability of a Me3NBH3 complex.
- Rabindranath Lo
- , Debashree Manna
- & Pavel Hobza