Attaching onto or Inserting into an Intramolecular Hydrogen Bond: Exploring and Controlling a Chirality-Dependent Dilemma for Alcohols DOI Open Access
Manuel Lange, Elisabeth Sennert, Martin A. Suhm

et al.

Published: Dec. 17, 2021

Prereactive complexes in noncovalent organocatalysis are sensitive to the relative chirality of binding partners and hydrogen bond isomerism. Both effects present when a transiently chiral alcohol docks on α-hydroxy ester, turning such 1:1 into elementary, non-reactive model systems for induction gas phase. With help linear infrared Raman spectroscopy supersonic jet expansions, conformational preferences investigated benzyl combination with methyl lactate, also exploring p-chlorination achiral homolog glycolate identify potential London dispersion energy sequence. Three four combinations prefer barrierless complexation via hydroxy group ester (association). In contrast, lightest complex shows predominantly insertion intramolecular bond, like analogous lactate methanol. The experimental findings rationalized computations uniform helicality by is predicted, independent or association internal bond. p-Chlorination has stabilizing effect association, because motif prevents close contact between chlorine ester. After simple anharmonicity substitution corrections, B3LYP-D3 approach offers fairly systematic description known spectroscopic data esters.

Language: Английский

Automated Molecular Cluster Growing for Explicit Solvation by Efficient Force Field and Tight Binding Methods DOI
Sebastian Spicher, Christoph Plett, Philipp Pracht

et al.

Journal of Chemical Theory and Computation, Journal Year: 2022, Volume and Issue: 18(5), P. 3174 - 3189

Published: April 28, 2022

An automated and broadly applicable workflow for the description of solvation effects in an explicit manner is introduced. This method, termed quantum cluster growth (QCG), based on semiempirical GFN2-xTB/GFN-FF methods, enabling efficient geometry optimizations MD simulations. Fast structure generation provided using intermolecular force field xTB-IFF. Additionally, approach uses implicit model electrostatic embedding growing clusters. The novel QCG procedure presents a robust tool subsequent application higher-level (e.g., DFT) methods to study molecular geometries explicitly or average spectroscopic properties over ensembles. Furthermore, computation free energy with supermolecular can be carried out QCG. underlying process physically motivated by computing leading-order solute-solvent interactions first account conformational chemical changes due low-energy barrier processes. space explored NCI-MTD algorithm as implemented CREST program, combination metadynamics GFN2-xTB yields realistic solution reasonable energies various systems without introducing many empirical parameters. Computed IR spectra some solutes show better match experimental data compared well-established models.

Language: Английский

Citations

89
Raman Optical Activity of N‐Acetyl‐L‐Cysteine in Water and in Methanol: The “Clusters‐in‐a‐Liquid” Model and ab Initio Molecular Dynamics Simulations DOI

Yanqing Yang,

Joseph Cheramy, Martin Brehm

et al.

ChemPhysChem, Journal Year: 2022, Volume and Issue: 23(11)

Published: March 30, 2022

Raman and Optical Activity (ROA) spectra of N-acetyl-L-cysteine (NALC), a flexible chiral molecule, were measured in water methanol to evaluate the solvent effects. Two different solvation approaches, that is, DFT based "clusters-in-a-liquid" model ab initio molecular dynamics (AIMD) simulations, applied simulate ROA spectra. Systematic conformational searches carried out using recently developed searching tool, CREST, with inclusion polarizable continuum methanol. The CREST candidates NALC NALC-solvent complexes re-optimized their simulations done at B3LYP-D3BJ/def2-TZVP B3LYP-aug-cc-pVDZ//cc-pVTZ levels. Also, AIMD which includes some anharmonic effects all intermolecular interactions solution, performed. By empirically weighting computed each conformer, good agreements experimental data achieved both while offered improvements carbonyl low wavenumber regions over static approach. pros cons these two approaches for accounting on this system will also be discussed.

Language: Английский

Citations

15
Setting up the HyDRA blind challenge for the microhydration of organic molecules DOI Creative Commons
Taija L. Fischer, Margarethe Bödecker, Anne Zehnacker

et al.

Physical Chemistry Chemical Physics, Journal Year: 2022, Volume and Issue: 24(19), P. 11442 - 11454

Published: Jan. 1, 2022

The first theory blind challenge addressing the effect of microsolvation on water vibrations is launched.

Language: Английский

Citations

13
Effect of binary fluid on the heat transfer performance of flat plate micro heat pipe DOI
Zhengang Zhao, Yingjun Feng, Chuan Luo

et al.

Applied Thermal Engineering, Journal Year: 2023, Volume and Issue: 235, P. 121304 - 121304

Published: Aug. 11, 2023

Language: Английский

Citations

7
Computer‐aided simulation of infrared spectra of ethanol conformations in gas, liquid and in CCl4 solution DOI
Sergey A. Katsyuba, Tatiana P. Gerasimova, Sebastian Spicher

et al.

Journal of Computational Chemistry, Journal Year: 2021, Volume and Issue: 43(4), P. 279 - 288

Published: Nov. 30, 2021

The recently developed efficient protocol combining implicit and explicit, accurate quantum-mechanical modeling of the condensed state (Katsyuba et al., J. Chem. Phys. 155, 024507 [2021]) is used to describe IR spectra liquid ethanol its solutions in CCl4 . relative abundance anti gauche conformers shown increase from ~40:60 gas phase ~55:45 phase. In spite a moderate impact media effects on conformational composition liquid, solvent strongly influences vibrational frequencies, intensities, normal modes each conformer, producing qualitatively different compared solution. Further, these affecting frequencies intensities depend not only conformation solvated molecule but also solvating species. Nevertheless, several isotopomers practically coincide with other. Convenient liquid-state markers fingerprint region are revealed for hydroxyl-deuterated species: CH3 CH2 OD, CHDOD, CD2 CD3 OD.

Language: Английский

Citations

15
Influence of microsolvation on vibrational circular dichroism spectra in dimethyl sulfoxide solvent: A Bottom-Up approach using Quantum cluster growth DOI
Andrew R. Puente, Prasad L. Polavarapu

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, Journal Year: 2023, Volume and Issue: 303, P. 123231 - 123231

Published: Aug. 2, 2023

Language: Английский

Citations

6
Infrared and vibrational circular dichroism spectra of methyl β‐D‐glucopyranose in water: The application of the quantum cluster growth and clusters‐in‐a‐liquid solvation models DOI Creative Commons

Angelo Shehan Perera,

Colton D. Carlson, Joseph Cheramy

et al.

Chirality, Journal Year: 2023, Volume and Issue: 35(10), P. 718 - 731

Published: May 10, 2023

The infrared (IR) and vibrational circular dichroism (VCD) spectra of methyl β-D-glucopyranose in water were measured. Both implicit explicit solvation models utilized to explain the observed spectra. vast body existing experimental theoretical data suggested that about eight molecules are needed account for solvent effects, supported by current Quantum Cluster Growth (QCG) analysis. Extensive manual systematic conformational searches molecular target its clusters carried out using a recently developed searching tool, conformer-rotamer ensemble sampling tool (CREST), microsolvation model associated QCG code. Boltzmann averaged IR VCD β-D-glucopyranose-(water)n (n = 8) conformers PCM provide better agreement with ones than those n 0, 1, 2. was shown greatly modify preference from monomeric form. Further analyses show result is consistent existence long-lived monohydrates additional effects being accounted quantum mechanical treatment other seven close-by water.

Language: Английский

Citations

5
Computational analysis of the vibrational spectra and structure of aqueous cytosine DOI
Sergey A. Katsyuba, Timur I. Burganov

Physical Chemistry Chemical Physics, Journal Year: 2023, Volume and Issue: 25(35), P. 24121 - 24128

Published: Jan. 1, 2023

The inclusion of 30 explicit water molecules in the quantum chemical model aqueous cytosine is sufficient to reproduce relative intensities and positions IR Raman bands spectra cytosine-d 3 .

Language: Английский

Citations

4
What quantum chemical simulations tell us about the infrared spectra, structure and interionic interactions of a bulk ionic liquid DOI
Sergey A. Katsyuba, Elena E. Zvereva

Physical Chemistry Chemical Physics, Journal Year: 2022, Volume and Issue: 24(12), P. 7349 - 7355

Published: Jan. 1, 2022

The recently developed efficient protocol to explicit quantum mechanical modeling of the structure and IR spectra liquids solutions [Katsyuba et al., J. Phys. Chem. B, 2020, 124, 6664-6670] is applied ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate [Emim][BF4], its C2-deuterated analog [Emim-d][BF4]. It shown that solvation strongly modifies frequencies intensities both cationic anionic components liquids. main features bulk are reproduced by simulations for cluster ([Emim][BF4])8, representing an ion pair solvated first shell. geometry closely resembles solid-state actual characterized short contacts all CH moieties imidazolium ring with [BF4]- anions. Both structural spectroscopic analyses allow be interpreted as hydrogen bonds approximately equal strength. enthalpies these liquid-state H-bonds, estimated use empirical correlations, amount 1.2-1.5 kcal mol-1, while analogous estimates obtained gas-phase charged species [Emim][BF4]2- [Emim]2[BF4]+ increase 3.6-3.9 mol-1.

Language: Английский

Citations

7
Computationally assisted vibrational spectroscopy of nucleic acid bases. 2. Thymine DOI
Sergey A. Katsyuba, Timur I. Burganov

Spectrochimica Acta Part A Molecular and Biomolecular Spectroscopy, Journal Year: 2024, Volume and Issue: 309, P. 123832 - 123832

Published: Jan. 4, 2024

Language: Английский

Citations

1