#physchem

@robpollice.mstdn.science.ap.brid.gy

2 weeks ago

#RobSelects paper of the week #ScienceMagazine: Single-molecule vibrational spectroscopy via tunable femtosecond infrared excitation and cryogenic ultra-high vacuum scanning tunneling microscopy. #physchem https://doi.org/10.1126/science.adz6643

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Peter Kenny

@pwk2024.bsky.social

1 month ago

Binding Entropy Can Be Predicted by Crystallographic Ensembles Protein-ligand binding is governed by free energy, comprising both enthalpic and entropic contributions. Yet structural interpretations of binding thermodynamics have predominantly focused on enthalpic interactions, largely neglecting entropy because it is difficult to quantify from static structural models. Here, we developed multiconformer ensemble models to analyze high-resolution X-ray crystallography structures and estimate both protein and solvent conformational entropies. These ensemble models successfully predicted experimental binding entropies measured by isothermal titration calorimetry for over 70 protein-ligand pairs across 12 proteins, revealing a strong linear correlation. Protein entropy, estimated using crystallographic order parameters that capture both harmonic and anharmonic motion, correlates linearly with experimental binding entropy. Incorporating resolution-corrected differences in water-molecule counts substantially improves predictions, demonstrating that protein and solvent contributions must be considered jointly. Analysis of water-protein hydrogen bonding networks partially explains entropic differences across complexes. These results establish that crystallographic ensembles can quantify binding entropy, enabling explicit entropic considerations in structure-based studies of molecular recognition for both functional analysis and drug design. ### Competing Interest Statement The authors have declared no competing interest. American Cancer Society, https://ror.org/02e463172

Miller & Wankowicz (2026) Binding Entropy Can Be Predicted by Crystallographic Ensembles. #bioRxiv #preprint #CompChem #PhysChem #biophys #cheminformatics #chemsky 🧪
doi.org/10.64898/202...

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Karel "CaCO3" Berka

@krapnik.bsky.social

2 months ago

BTW: Transition energy is 118.43 kcal/mol in vacuo with OMol25's eSEN Conserving Small model.

Not that much - those Christmas cookie eating should do the job... :)

#theochem #compchem #chemsky ⚛️🧪 #RareEvent #EnhancedSampling #PathSampling #PhysChem #chemchat #Chemistry #ChemBio #EdTech

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ČervinkaGroup

@cervinkagroup.bsky.social

2 months ago

Home - BEST-CSP | COST Action CA22107 BEST-CSP | COST Action CA22107. Bringing Experiment and Simulation Together in Crystal Structure Prediction.

We are taking up a challenge with the #BEST-CSP blind test of predictions of physical properties of #molecular_crystals. Let's see what we can achieve before May. best-csp.eu #COSTactions #CompChem #PhysChem

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Peter Kenny

@pwk2024.bsky.social

3 months ago

CSIRO Postdoctoral Fellowship in CO2 Capture and Utilisation CSIRO Postdoctoral Fellowship in CO2 Capture and Utilisation

#PostDoc in #CO2 capture and utilisation at CSIRO (Newcastle NSW Australia) ref: 101876 | duration: 3 years | closing: 19-Jan-2026 #PhysChem #AnalChem #chemsky 🧪
jobs.csiro.au/job/Newcastl...

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ČervinkaGroup

@cervinkagroup.bsky.social

3 months ago

Introducing the Coupled-Cluster Theory to the Amorphous World of Liquids and Their Thermodynamic Simulations Amorphous molecular materials are ubiquitous, spanning drugs, semiconductors, or solvents. Large predictive capabilities of quantum-chemical simulations of structural and thermodynamic properties and ...

Read about how we tamed bulk molecular liquids by Monte Carlo simulations and the coupled-clusters theory. Now in #JCTC by @pubs.acs.org. #compchem #physchem pubs.acs.org/doi/full/10....

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Peter Kenny

@pwk2024.bsky.social

3 months ago

Decades later, a Yale chemist’s water simulations continue to make waves A look back at one of the most cited science studies of all time — Sterling Professor of Chemistry William Jorgensen’s landmark 1983 simulations of water.

Water, water everywhere... #PhysChem #CompChem #cheminformatics #chemsky 🧪
news.yale.edu/2025/11/18/d...

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Department of Physical and Macromolecular Chemistry

@kfmch.bsky.social

4 months ago

The Nanomaterials Modelling Group studied laser pulse driven ultrafast dynamics in diverse magnets — FM, AFM, and emerging altermagnets — under different light polarization angles using state-of-the-art real time TDDFT theory.

doi.org/10.1021/acs....

#PhysicalChemistry #PhysChem #QuantumChemistry

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Robert Pollice

@robpollice.mstdn.science.ap.brid.gy

5 months ago

#RobSelects paper of the week #J_A_C_S: X-ray induced Coulomb explosion imaging of the hydrogen atom positions in individual thiophenone molecules. #physchem https://doi.org/10.1021/jacs.5c08730

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Peter Kenny

@pwk2024.bsky.social

6 months ago

Early Formulation Science and Drug Delivery (EFS-DD) Senior Principal Scientist Use Your Power for Purpose This Senior Principal Scientist position will be a strong scientific and leadership role within the Early Formulation Science and Drug Delivery (EFS-DD) group, supporting ea...

Opportunity in formulation and drug delivery at Pfizer (Cambridge MA USA) ref: 4940149 #PharmSci #PhysChem #ChemJobs #chemsky 🧪
pfizer.wd1.myworkdayjobs.com/PfizerCareer...

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Peter Kenny

@pwk2024.bsky.social

7 months ago

Unveiling Repulsion in Intramolecular H-Bonded Systems Intramolecular H-bonds govern molecular conformation and play critical roles in pharmaceutical design, catalysis, and supramolecular chemistry. Despite this, the experimental influence of ortho-substi...

Worth reading if trying to exploit intramolecular hydrogen bonding in #ADME optimization: Smolyar & Cockroft (2025) Unveiling Repulsion in Intramolecular H-Bonded Systems. JACS 47:12381-12385 #Hbond #PhysChem #DrugDesign #MedChem #cheminformatics #OpenAccess #chemsky 🧪
doi.org/10.1021/jacs...

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Tom Fay

@tompfay.bsky.social

7 months ago

#theoreticalchemistry #theochem #chemistry #quantum #quantumbiology #physchem

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Daniele Fazzi

@dfazzi82.bsky.social

8 months ago

Last week I received the best lecture award at the physical chemistry conference CDCF50 & ECPC, in Pisa. Very much honoured! A special thanks to my students and collaborators for the exciting work! @tide-rtg.bsky.social #softmatter #compchem #physchem

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Daniele Fazzi

@dfazzi82.bsky.social

8 months ago

Attending CDCF50 and ECPC in wonderful Pisa. I gave a talk today on modelling disorder effects in organic soft materials. A lot of interesting interactions and contributions!
#softmatter #chemcomp #physchem

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ČervinkaGroup

@cervinkagroup.bsky.social

8 months ago

We are at #WATOC2025! Presenting two contributions about our development of #AbInitio #MonteCarlo simulations for molecular liquids and about peculiarities of #CrystalStructurePrediction for #IonicLiquids. #CompChem #PhysChem

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ČervinkaGroup

@cervinkagroup.bsky.social

8 months ago

A seal of excellence for our fresh graduate student Veronika! She was awarded with the Josef Novák prize at @vschtpraha.bsky.social for her Master thesis dealing with #molecular_dynamics simulations of inner dynamics and glass transitions in #porous_liquids. Congrats! #CompChem #PhysChem

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Peter Kenny

@pwk2024.bsky.social

8 months ago

Scientist – Biophysical Vernalis collaborates with a wide range of organisations to enable drug discovery programs through both short- and long-term projects

Opportunity for biophysical scientist at Vernalis (Cambridge UK) #biochem #biophysics #assay #AnalChem #PhysChem #UKChemJobs #ChemJobs #chemsky 🧪
www.vernalis.com/vacancies/sc...

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Peter Kenny

@pwk2024.bsky.social

9 months ago

Thinking About Aqueous Solvation Given that it was International Women's Day yesterday, I'll open the the post (and blogging for 2025) with a photo of a gravestone at St Jam...

Reposting some thoughts on alkane/water #logP and aqueous solvation #PhysChem #MedChem #cheminformatics #chemsky 🧪
fbdd-lit.blogspot.com/2025/03/thin...

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ČervinkaGroup

@cervinkagroup.bsky.social

9 months ago

Today contributing to #MQM2025 in #Kyoto! Representing the #EcoStore project solved at @vschtpraha.bsky.social and promoting our recent work about efficient in silico modeling of #molecular_crystals from #jctc @pubs.acs.org: pubs.acs.org/doi/10.1021/... #CompChem #PhysChem

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Peter Kenny

@pwk2024.bsky.social

9 months ago

Lose Your Crystalline Form and Go Amorphous #InThePipeline #PhysChem #MedChem #cheminformatics #chemsky 🧪

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ČervinkaGroup

@cervinkagroup.bsky.social

9 months ago

Dynamic disorder in #molecular_crystals can be a good servant, but also a bad master! Read more in our new highlight paper in @crystengcomm.rsc.org #compchem #physchem
pubs.rsc.org/en/content/a...

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IOCB Prague

@iocbprague.bsky.social

9 months ago

🧪 Výzkumný tým vedený prof. Pavlem Jungwirthem z @iocbprague.bsky.social @czechacademy.bsky.social zjistil, že během procesu, kdy se kapalina mění z nekovu na vodivý kov, vzniká ještě jeden, zatím nepopsaný jev. 🧵

#physchem #compchem #iocbprague #iocb #czechscience #akademievedcr

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Peter Kenny

@pwk2024.bsky.social

9 months ago

(EPSRC DTP) Combining experiment and theory to understand dynamic ordering of molecules in liquid solutions that influences physical properties of drug-like molecules and reactivity at The University ... PhD Project - (EPSRC DTP) Combining experiment and theory to understand dynamic ordering of molecules in liquid solutions that influences physical properties of drug-like molecules and reactivity at T...

Funded #PhD opportunity: experiment & theory to understand dynamic ordering of drug-like molecules in liquid solutions at University of Manchester (UK) funding: 3.5 years | closing: 02-Jun-2025 #PhysChem #biophysics #CompChem #cheminformatics #ChemPhD #chemsky 🧪
www.findaphd.com/phds/project...

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Robert Pollice

@robpollice.mstdn.science.ap.brid.gy

10 months ago

#RobSelects paper of the week #J_A_C_S: Detailed investigation of the methyl lactate van der Waals dimers via jet-cooled rotational spectroscopy. #physchem https://doi.org/10.1021/jacs.5c01184

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Jorge Luis Gálvez Vallejo

@jorgegalvez.bsky.social

11 months ago

The link to register for the talk in the first post! Feel free to come by and share with your networks!
#compchem #physchem

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Robert Pollice

@robpollice.mstdn.science.ap.brid.gy

11 months ago

Hydrogen activation by a σσ*-carbene through quantum tunneling The electronic structure of carbenes arises from the occupation of a σ and a π frontier orbital. While parent methylene possesses a triplet ground state (σ1π1), substituents are capable of stabilizing the singlet (σ2π0 or σ0π2) by altering the frontier orbital energies. Here, we reveal that the 1,2[I]-shift isomer of 2-iodopyridine, the N-iodo Hammick intermediate, features a resonance between its carbene σ and N–I bond σ* orbitals, rendering them frontier orbitals. This singlet carbene is efficiently generated via UV photolysis of 2-iodopyridine in solid neon at 4.4 K and reacts with molecular hydrogen − but not deuterium − via N–I bond cleavage enabled by quantum tunnelling. Our findings introduce an unprecedented carbene class, unlocking new opportunities for reactivity and electronic structure explorations.

#RobSelects preprint of the week #ChemRxiv: The N-iodo Hammick intermediate of reacts as a carbene via cleavage of the nitrogen-iodine bond. #physchem https://doi.org/10.26434/chemrxiv-2025-bf6qk

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Peter Kenny

@pwk2024.bsky.social

1 year ago

To kick off blogging for 2025 here is a post on aqueous #solvation and alkane/water #logP #PhysChem #CompChem #cheminformatics #MedChem #DrugDesign #DrugDiscovery #ADME #chemsky 🧪
fbdd-lit.blogspot.com/2025/03/thin...

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Esther Johnston

@estherjohnston.bsky.social

1 year ago

#theoreticalchemistry #compchem #physchem

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Peter Kenny

@pwk2024.bsky.social

1 year ago

The Cation−π Interaction in Chemistry and Biology The cation−π interaction is an important noncovalent binding force that impacts all areas of chemistry and biology. Extensive computational and gas phase experimental studies have established the pote...

Dougherty (Chem Rev 2025 ASAP) The Cation−π Interaction in Chemistry and Biology (currently free to read) #PhysChem #CompChem #cheminformatics #chemsky 🧪
doi.org/10.1021/acs....

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Posts tagged #physchem