OpenMolcas: From Source Code to Insight

Journal of Chemical Theory and Computation, Год журнала: 2019, Номер 15(11), С. 5925 - 5964

Опубликована: Сен. 11, 2019

In this Article we describe the OpenMolcas environment and invite computational chemistry community to collaborate. The open-source project already includes a large number of new developments realized during transition from commercial MOLCAS product platform. paper initially describes technical details software development This is followed by brief presentations many methods, implementations, features program suite. These include novel wave function methods such as stochastic complete active space self-consistent field, density matrix renormalization group (DMRG) hybrid multiconfigurational functional theory models. Some these implementations an array additional options functionalities. proceeds related explorations potential energy surfaces. Here present for optimization conical intersections, simulation adiabatic nonadiabatic molecular dynamics, interfaces tools semiclassical quantum mechanical nuclear dynamics. Furthermore, unique simulations spectroscopic magnetic phenomena exact description interaction between light matter, various X-ray processes, circular dichroism, properties. Finally, built-in add-on support platform with postcalculation analysis visualization, multiscale option using frozen-density embedding theory, electronic muonic basis sets.

Язык: Английский

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Multireference Approaches for Excited States of Molecules

Chemical Reviews, Год журнала: 2018, Номер 118(15), С. 7293 - 7361

Опубликована: Июль 24, 2018

Understanding the properties of electronically excited states is a challenging task that becomes increasingly important for numerous applications in chemistry, molecular physics, biology, and materials science. A substantial impact exerted by fascinating progress time-resolved spectroscopy, which leads to strongly growing demand theoretical methods describe characteristic features accurately. Whereas electronic ground state problems stable molecules quantum chemical methodology now so well developed informed nonexperts can use it efficiently, situation entirely different concerning investigation states. This review devoted specific class approaches, usually denoted as multireference (MR) methods, generality needed solving many spectroscopic or photodynamical problems. However, understanding proper application these MR often found be difficult due their complexity computational cost. The purpose this provide an overview most facts about approaches available present means collection examples useful information, guide reader performing own applications.

Язык: Английский

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Advances in theE → ZIsomerization of Alkenes Using Small Molecule Photocatalysts

Chemical Reviews, Год журнала: 2021, Номер 122(2), С. 2650 - 2694

Опубликована: Авг. 27, 2021

Geometrical E → Z alkene isomerization is intimately entwined in the historical fabric of organic photochemistry and enjoying a renaissance (Roth et al. Angew. Chem., Int. Ed. Engl. 1989 28, 1193–1207). This consequence fundamental stereochemical importance Z-alkenes, juxtaposed with frustrations thermal reactivity that are rooted microscopic reversibility. Accessing excited state paradigms allow this latter obstacle to be circumnavigated by exploiting subtle differences photophysical behavior substrate product chromophores: provides molecular basis for directionality. While direct irradiation operationally simple, photosensitization via selective energy transfer enables augmentation repertoire include substrates not directly photons. Through sustained innovation, an impressive portfolio tailored small molecule catalysts range triplet energies now widely available facilitate contra-thermodynamic thermo-neutral reactions generate Z-alkene fragments. review intended serve as practical guide covering geometric alkenes enabled catalysis from 2000 2020, logical sequel excellent treatment Dugave Demange (Chem. Rev. 2003 103, 2475–2532). The mechanistic foundations underpinning selectivity discussed together induction models rationales explain counterintuitive directionality these processes which very distinguish product. Implications subsequent stereospecific transformations, application total synthesis, regioselective polyene isomerization, spatiotemporal control pre-existing configuration broader sense discussed.

Язык: Английский

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Molecular excited states through a machine learning lens

Nature Reviews Chemistry, Год журнала: 2021, Номер 5(6), С. 388 - 405

Опубликована: Май 20, 2021

Язык: Английский

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A General Strategy to Control Viscosity Sensitivity of Molecular Rotor‐Based Fluorophores

Angewandte Chemie International Edition, Год журнала: 2020, Номер 60(3), С. 1339 - 1346

Опубликована: Сен. 29, 2020

Molecular rotor-based fluorophores (RBFs) have been widely used in many fields. However, the lack of control their viscosity sensitivity limits application. Herein, this problem is resolved by chemically installing extended π-rich alternating carbon-carbon linkages between rotational electron donors and acceptors RBFs. The data reveal that length linkage strongly influences sensitivity, likely resulting from varying height energy barriers fluorescent planar dark twisted configurations. Three RBF derivatives span a wide range sensitivities were designed. These RBFs demonstrated, through dual-color imaging strategy, they can differentiate misfolded protein oligomers insoluble aggregates, both test tubes live cells. Beyond RBFs, it envisioned chemical mechanism might be generally applicable to photoisomerizable aggregation-induced emission fluorophores.

Язык: Английский

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Three-dimensional view of ultrafast dynamics in photoexcited bacteriorhodopsin

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Июль 18, 2019

Abstract Bacteriorhodopsin (bR) is a light-driven proton pump. The primary photochemical event upon light absorption isomerization of the retinal chromophore. Here we used time-resolved crystallography at an X-ray free-electron laser to follow structural changes in multiphoton-excited bR from 250 femtoseconds 10 picoseconds. Quantum chemistry and ultrafast spectroscopy were identify sequential two-photon process, leading excitation tryptophan residue flanking chromophore, as first manifestation multiphoton effects. We resolve distinct stages dynamics all- trans photoexcited highly twisted 13- cis conformation. Other active site sub-picosecond rearrangements include correlated vibrational motions electronically excited surrounding amino acids water molecules well their hydrogen bonding network. These results show that this extended photo-active network forms vibrationally coupled system bR, most likely all proteins.

Язык: Английский

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Molecular Photochemistry: Recent Developments in Theory

Angewandte Chemie International Edition, Год журнала: 2020, Номер 59(39), С. 16832 - 16846

Опубликована: Фев. 13, 2020

Photochemistry is a fascinating branch of chemistry that concerned with molecules and light. However, the importance simulating light-induced processes reflected also in fields as diverse biology, material science, medicine. This Minireview highlights recent progress achieved theoretical to calculate electronically excited states simulate their photoinduced dynamics, aim reaching experimental accuracy. We focus on emergent methods give selected examples illustrate years towards predicting complex electronic structures strong correlation, calculations large molecules, describing multichromophoric systems, non-adiabatic molecular dynamics over long time scales, for gas phase or biological environments.

Язык: Английский

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Advances and challenges in time-resolved macromolecular crystallography

Science, Год журнала: 2021, Номер 373(6558)

Опубликована: Авг. 26, 2021

Bright future ahead for crystallography Macromolecular x-ray typically provides static snapshots of systems at equilibrium. Advances in time-resolved have made it possible to capture dynamics biomolecules: large and small, fast slow. Brändén Neutze review techniques concepts that emerged from recent work free electron laser sources are now being applied other settings a growing number biological systems. Despite challenges analyzing relating these data context, experiments this field opened new frontiers temporal spatial resolution yielded many insights into nonequilibrium chemistry conformational changes biology. —MAF

Язык: Английский

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Restriction of Intramolecular Motion(RIM): Investigating AIE Mechanism from Experimental and Theoretical Studies

Chemical Research in Chinese Universities, Год журнала: 2021, Номер 37(1), С. 1 - 15

Опубликована: Янв. 15, 2021

Язык: Английский

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Ultrafast structural changes direct the first molecular events of vision

Nature, Год журнала: 2023, Номер 615(7954), С. 939 - 944

Опубликована: Март 22, 2023

Abstract Vision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs) 1 . A photon absorbed 11- cis retinal chromophore rhodopsin, which isomerizes within 200 femtoseconds to all- trans conformation 2 , thereby initiating cellular signal transduction processes that ultimately lead vision. However, intramolecular mechanism photoactivated induces activation events inside remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature 3 determine how an isomerized twisted all -trans stores energy required initiate protein conformational changes associated with formation protein-binding signalling state. The distorted a 1-ps time delay after photoactivation has pulled away from half its numerous interactions binding pocket, and excess released through anisotropic breathing motion in direction extracellular space. Notably, very early structural motions side chains appear regions are involved later stages conserved class GPCR mechanism. Our study sheds light on earliest vision vertebrates points fundamental aspects molecular mechanisms agonist-mediated activation.

Язык: Английский

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