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Modelling the dynamics of crowded enzymes

04 Apr 2012

The folding of proteins in a living cell is affected by all the other species present in the cell which can get in the way. Hence studying protein folding in solution does not give a full picture of what really happens in cells.

Raymond Kapral and Carlos Echeverriaab working at the University of Toronto and the Universidad de Los Andes used computer simulations to understand the effects of crowding on the folding of the adenylate kinase protein.

They found that when there were a lot of obstacles present along with the protein it was more likely to be in a closed confirmation, and interestingly that small obstacles could interact with the protein so that it was locked in an open confirmation.

The authors suggest that their method could be extended to provide further information on protein dynamics in more realistic models of crowded systems.

Read this HOT article today:

Molecular crowding and protein enzymatic dynamics
Carlos Echeverria and Raymond Kapral
Phys. Chem. Chem. Phys., 2012, DOI: 10.1039/C2CP40200A

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Thermo-Hilger Award and Allan Ure Bursary – nominations open

02 Apr 2012

The Thermo-Hilger Award and Allan Ure Bursary are now open for nominations or applications.

Closing date: 30 April 2012

The Thermo-Hilger Award is presented biennially to an RSC member in the early stages of their career who uses atomic spectrometry during their work.

The winner receives a cash/book prize and free registration (including meals, events and conference dinner) to attend a major national conference on atomic spectroscopy.

The Allan Ure Bursary is awarded annually to a scientist, at the start of their career, who has made a significant contribution to the application of atomic spectrometry to environmental science.

The successful applicant will receive £500 to help with any expenses that may be of benefit to their career. For example, this could be to travel to or attend a conference, so that they may present their work.

More details about the prizes and how to apply can be found on the Atomic Spectroscopy Group Awards page.

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ICPOC21: oral abstract submission deadline 13th April

02 Apr 2012

Good news!

There’s still a chance to submit your oral abstract to ICPOC21: 21^st IUPAC International Conference on Physical Organic Chemistry to be held 9 – 13 September 2012 at Durham University.

The Scientific Committee is currently reviewing all submissions, and has agreed to accept contributions up to Friday 13 April to allow for the Easter holiday break.

Why join ICPOC21?

This meeting is organised by the Organic Division of the RSC on behalf of IUPAC. In addition to outstanding plenary sessions, there will be three parallel sessions over the five days comprising invited lectures and contributed talks, as well as poster sessions.

Key topics that will be covered in the meeting include:

Physical underpinnings
Mechanism and catalysis
Supramolecular and systems chemistry

A broad range of scientists from across the whole community who share a quantitative perspective on chemistry will be there, providing an opportunity to discuss and celebrate the current status, development, and the future of physical organic chemistry.

Make sure you are one of them! Don’t miss the oral abstract submission deadline – 13 April.

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German Bunsen-Society Prize: Nominations Open

21 Mar 2012

Deutsche Bunsen-Gesellschaft für Physikalische Chemie
awards the

Nernst-Haber-Bodenstein Prize 2013

in memory of Max Bodenstein, Fritz Haber and Walter Nernst. The prize will be presented at the 112th Annual General Meeting of the German Bunsen-Society from 9 -11 May 2013 in Karlsruhe.

The prize will be awarded to a distinguished younger scientist (of up to 40 years of age) for outstanding scientific achievements in the field of physical chemistry. Suitable candidates of international visibility in their research field will be evaluated by a high level expert selection panel with respect to the scientific quality, originality and independence of their research. Candidates should come from a German-speaking region of Europe or work there at the time of their nomination.

Nominations from established scientists in the area of physical chemistry should include a short CV of the candidate, an overview of the candidate’s scientific achievements and publications, and a supporting statement.

Nominations should be submitted by 1 October 2012 to:

Deutsche Bunsen Gesellschaft
für Physikalische Chemie e.V.
Erika Wöhler
Theodor-Heuss-Allee 25
60486 Frankfurt am Main
Germany

View the PCCP themed issue just published on Interfaces of ionic liquids, Guest Edited by Frank Endres, which will be displayed as the special Bunsen issue at the DBG annual meeting in May 2012.

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Isotopic studies reveal new insights into supercritical CO2

29 Feb 2012

Scientists from the Pacific Northwest National Laboratory (PNNL) in the USA have studied the Raman spectrum of supercritical ¹⁸O-labelled CO₂and discovered that its vibrational modes were different to that of supercritical CO₂ containing the more abundant ¹⁶O isotope. You can read a press release about the work from PNNL here.

Read the full article today:

Raman spectrum of supercritical C¹⁸O₂ and re-evaluation of the Fermi resonance
Charles F. Windisch , Vassiliki-Alexandra Glezakou , Paul F. Martin , B. Peter McGrail and Herbert T. Schaef
Phys. Chem. Chem. Phys., 2012, 14, 2560-2566
DOI: 10.1039/C1CP22349F

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Most-read in 2011 – what was hot in PCCP last year?

14 Feb 2012

Top 25 most-read PCCP articles for 2011

Density functional theory for transition metals and transition metal chemistry
Christopher J. Cramer and Donald G. Truhlar
DOI: 10.1039/B907148B

Density functional theory for transition metals and transition metal chemistry

Titania supported gold nanoparticles as photocatalyst
Ana Primo, Avelino Corma and Hermenegildo García
DOI: 10.1039/C0CP00917B

Colloidal metal nanoparticles as a component of designed catalyst
Chun-Jiang Jia and Ferdi Schüth
DOI: 10.1039/C0CP02680H

Studying disorder in graphite-based systems by Raman spectroscopy
M. A. Pimenta, G. Dresselhaus, M. S. Dresselhaus, L. G. Cançado, A. Jorio and R. Saito
DOI: 10.1039/B613962K

Layer-by-layer assembly as a versatile bottom-up nanofabrication technique for exploratory research and realistic application
Katsuhiko Ariga, Jonathan P. Hill and Qingmin Ji
DOI: 10.1039/B700410A

Air and water stable ionic liquids in physical chemistry
Frank Endres and Sherif Zein El Abedin
DOI: 10.1039/B600519P

Carbon materials for supercapacitor application
Elzbieta Frackowiak
DOI: 10.1039/B618139M

Characterization of nanostructured hybrid and organic solar cells by impedance spectroscopy
Francisco Fabregat-Santiago, Germà Garcia-Belmonte, Iván Mora-Seró and Juan Bisquert
DOI: 10.1039/C0CP02249G

Catalysis by metal–organic frameworks: fundamentals and opportunities
Marco Ranocchiari and Jeroen Anton van Bokhoven
DOI: 10.1039/C0CP02394A

A thorough benchmark of density functional methods for general main group thermochemistry, kinetics, and noncovalent interactions
Lars Goerigk and Stefan Grimme
DOI: 10.1039/C0CP02984J

Graphene-based electrochemical energy conversion and storage: fuel cells, supercapacitors and lithium ion batteries
Junbo Hou, Yuyan Shao, Michael W. Ellis, Robert B. Moore and Baolian Yi
DOI: 10.1039/C1CP21915D

Bimetallic Pt–Au nanocatalysts electrochemically deposited on graphene and their electrocatalytic characteristics towards oxygen reduction and methanol oxidation
Yaojuan Hu, Hua Zhang, Ping Wu, Hui Zhang, Bo Zhou and Chenxin Cai
DOI: 10.1039/C0CP01998D

Recent progress in SERS biosensing
Kyle C. Bantz, Audrey F. Meyer, Nathan J. Wittenberg, Hyungsoon Im, Özge Kurtuluş, Si Hoon Lee, Nathan C. Lindquist, Sang-Hyun Oh and Christy L. Haynes
DOI: 10.1039/C0CP01841D

Fullerene derivative acceptors for high performance polymer solar cells
Youjun He and Yongfang Li
DOI: 10.1039/C0CP01178A

Molecular states of water in room temperature ionic liquids
L. Cammarata, S. G. Kazarian, P. A. Salter and T. Welton
DOI: 10.1039/B106900D

Sandwich-type functionalized graphene sheet-sulfur nanocomposite for rechargeable lithium batteries
Yuliang Cao, Xiaolin Li, Ilhan A. Aksay, John Lemmon, Zimin Nie, Zhenguo Yang and Jun Liu
DOI: 10.1039/C0CP02477E

Nanostructured polymer assemblies formed at interfaces: applications from immobilization and encapsulation to stimuli-responsive release
Yajun Wang, Leticia Hosta-Rigau, Hannah Lomas and Frank Caruso
DOI: 10.1039/C0CP02287J

Formation of chains of graphitic nanoparticles by heating fullerene blacks covered with thin metal films
H. Kanzow, A. Ding, J. Nissen, H. Sauer, T. Belz and R. Schlögl
DOI: 10.1039/B002735I

Fe₃O₄nanoparticle-integrated graphene sheets for high-performance half and full lithium ion cells
Liwen Ji, Zhongkui Tan, Tevye R. Kuykendall, Shaul Aloni, Shidi Xun, Eric Lin, Vincent Battaglia and Yuegang Zhang
DOI: 10.1039/C1CP20455F

New nanostructured heterogeneous catalysts with increased selectivity and stability
Ilkeun Lee, Manuel A. Albiter, Qiao Zhang, Jianping Ge, Yadong Yin and Francisco Zaera
DOI: 10.1039/C0CP01688H

Photoblinking and photobleaching of rylene diimide dyes
Mathias Haase, Christian G. Hübner, Fabian Nolde, Klaus Müllen and Thomas Basché
DOI: 10.1039/C0CP01814G

Electrocatalysis of oxygen reduction and small alcohol oxidation in alkaline media
Jacob S. Spendelow and Andrzej Wieckowski
DOI: 10.1039/B703315J

Oriented attachment and mesocrystals: Non-classical crystallization mechanisms based on nanoparticle assembly
Markus Niederberger and Helmut Cölfen
DOI: 10.1039/B604589H

Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
Petr Jurečka, Jiří Šponer, Jiří Černý and Pavel Hobza
DOI: 10.1039/B600027D

Application of ionic liquids to the electrodeposition of metals
Andrew P. Abbott and Katy J. McKenzie
DOI: 10.1039/B607329H

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High impact Perspectives from PCCP

07 Feb 2012

We would like to share with you some of the high impact Perspective articles which have been published in Physical Chemistry Chemical Physics (PCCP) in 2011.

Offering new insights and authoritative state-of-the-art accounts across the journal’s broad scope, PCCP Perspectives are of the highest quality and impact.

On behalf of the Editorial Board of PCCP we invite you to submit your research today.

Read a selection of our high impact Perspectives:

Operation of micro and molecular machines: a new concept with its origins in interface science
Katsuhiko Ariga, Shinsuke Ishihara, Hironori Izawa, Hong Xia and Jonathan P. Hill
DOI: 10.1039/C0CP02040K

The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates
Motohiro Nishio
DOI: 10.1039/C1CP20404A

Towards large-scale, fully ab initio calculations of ionic liquids
Ekaterina I. Izgorodina
DOI: 10.1039/C0CP02315A

Catalysis by metal–organic frameworks: fundamentals and opportunities
Marco Ranocchiari and Jeroen Anton van Bokhoven
DOI: 10.1039/C0CP02394A

Hofmeister effects: interplay of hydration, nonelectrostatic potentials, and ion size
Drew F. Parsons, Mathias Boström, Pierandrea Lo Nostro and Barry W. Ninham
DOI: 10.1039/C1CP20538B

Electronic structure in real time: mapping valence electron rearrangements during chemical reactions
Philippe Wernet
DOI: 10.1039/C0CP02934C

Weak H-bonds. Comparisons of CH^…O to NH^…O in proteins and PH^…N to direct P^…N interactions
Steve Scheiner
DOI: 10.1039/C1CP20427K

Seeing the forest for the trees: fluorescence studies of single enzymes in the context of ensemble experiments
Yan-Wen Tan and Haw Yang
DOI: 10.1039/C0CP02412K

Multiply-charged ions and interstellar chemistry
Diethard Kurt Böhme
DOI: 10.1039/C1CP21814J

Nanoconfinement effects in energy storage materials
Maximilian Fichtner
DOI: 10.1039/C1CP22547B

Electrostatic interactions in biological DNA-related systems
A. G. Cherstvy
DOI: 10.1039/C0CP02796K

Do we fully understand what controls chemical selectivity?
Julia Rehbein and Barry K. Carpenter
DOI: 10.1039/C1CP22565K

Plasma electrochemistry in ionic liquids: an alternative route to generate nanoparticles
Oliver Höfft and Frank Endres
DOI: 10.1039/C1CP20501C

Time-resolved photoelectron spectroscopy: from wavepackets to observables
Guorong Wu, Paul Hockett and Albert Stolow
DOI: 10.1039/C1CP22031D

Structural and dynamic properties of oxygen vacancies in perovskite oxides—analysis of defect chemistry by modern multi-frequency and pulsed EPR techniques
Rüdiger-A. Eichel
DOI: 10.1039/B918782K

The yin and yang of amyloid: insights from α-synuclein and repeat domain of Pmel17
Ryan P. McGlinchey, Thai Leong Yap and Jennifer C. Lee
DOI: 10.1039/C1CP21376H

High to ultra-high power electrical energy storage
Stefanie A. Sherrill, Parag Banerjee, Gary W. Rubloff and Sang Bok Lee
DOI: 10.1039/C1CP22659B

Patchy colloids: state of the art and perspectives
Emanuela Bianchi, Ronald Blaak and Christos N. Likos
DOI: 10.1039/C0CP02296A

The mystery of gold’s chemical activity: local bonding, morphology and reactivity of atomic oxygen
Thomas A. Baker, Xiaoying Liu and Cynthia M. Friend
DOI: 10.1039/C0CP01514H

The ab initio calculation of molecular electric, magnetic and geometric properties
Radovan Bast, Ulf Ekström, Bin Gao, Trygve Helgaker, Kenneth Ruud and Andreas J. Thorvaldsen
DOI: 10.1039/C0CP01647K

Fullerene derivative acceptors for high performance polymer solar cells
Youjun He and Yongfang Li
DOI: 10.1039/C0CP01178A

Colloidal metal nanoparticles as a component of designed catalyst
Chun-Jiang Jia and Ferdi Schüth
DOI: 10.1039/C0CP02680H

Diffusion models of protein folding
Robert B. Best and Gerhard Hummer
DOI: 10.1039/C1CP21541H

You can find many more excellent Perspectives on our website.

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Operando surface spectroscopy themed issue out now!

02 Feb 2012

We are delighted to announce that the PCCP themed issue on Operando surface spectroscopy has now been published online – take a look today!

The issue was Guest Edited by C. O. Arean, B. M. Weckhuysenb and A. Zecchina – take a look at their Editorial.

The Operando surface spectroscopy themed issue features a broad range of papers and Communications and includes the following articles:

Operando surface spectroscopy—placing catalytic solids at work under the spotlight
C. O. Arean, B. M. Weckhuysen and A. Zecchina
Phys. Chem. Chem. Phys., 2012, 14, 2125-2127
DOI: 10.1039/C2CP90005J

Formation and oxidation mechanisms of Pd–Zn nanoparticles on a ZnO supported Pd catalyst studied by in situ time-resolved QXAFS and DXAFS
Yohei Uemura, Yasuhiro Inada, Yasuhiro Niwa, Masao Kimura, Kyoko K. Bando, Akira Yagishita, Yasuhiro Iwasawa and Masaharu Nomura
Phys. Chem. Chem. Phys., 2012, 14, 2152-2158
DOI: 10.1039/C1CP22466B

Low absorption vitreous carbon reactors for operando XAS: a case study on Cu/Zeolites for selective catalytic reduction of NOx by NH₃
Vincent F. Kispersky, A. Jeremy Kropf, Fabio H. Ribeiro and Jeffrey T. Miller
Phys. Chem. Chem. Phys., 2012, 14, 2229-2238
DOI: 10.1039/C1CP22992C

Take a look at the issue today!

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Molecular dynamics to combat chemical terrorism: PCCP article in Chemistry World

31 Jan 2012

Computers can make finding new ways of decontaminating the deadliest known chemicals safer and easier, according to US researchers.

VX (O-ethyl S-[2-(diisopropylamino)ethyl] methylphosphonothioate), made infamous by the 1996 Nicolas Cage film The Rock, is the most toxic nerve agent known and is also highly persistent. Although banned by the Chemical Weapons Convention, it is still important to understand and find new decontamination pathways to counter the threat of terrorism. However, traditionally, this is a very hazardous endeavour.

Interested to know more? Read the full article in Chemistry World here…

PCCP paper:
First-principles molecular dynamics simulations of condensed phase V-type nerve agent reaction pathways and energy barriers
Richard Gee , I-Feng William Kuo , Sarah C. Chinn and Ellen Raber
Phys. Chem. Chem. Phys., 2012, Accepted Manuscript
DOI: 10.1039/C2CP23126C

Fancy submitting an article to PCCP? Then why not submit to us today!

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Theoretical Chemistry Group Poster Prizes

30 Jan 2012

PCCP was delighted to sponsor two ‘PCCP Poster Prizes’ at the RSC Theoretical Chemistry Group Conference which was held at the University of Nottingham, June 27th – 29th 2011. Visit their website to find out more about the conference and the groups activities.

PCCP Poster Prize winners Ragnar Bjornsson (left) and David Mandive-Tapia (right)

The winners were David Mandive-Tapia (Imperial College London) for a poster entitled “Controlling the mechanism of fulvene S1/S0 decay” and Ragnar Bjornsson (St Andrews) for his poster on “The conformational properties of a flexible zwitterion, 3F-GABA, in solution: QM/MM MD simulations”.

PCCP will be awarding more Poster Prizes this year, so please do let us know of any suitable conferences which PCCP could sponsor in 2012.

Submit your lastest research to PCCP today!

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