Thursday, 29 September 2011

Phd: Development of a QM/MM Docking Code, Switzerland

Computational techniques including docking have become valuable tools for
drug design over the last decades. Main challenges for docking algorithms
include the accurate treatment of polarization and covalent interactions,
for example with transition metal ions, which need to be described on the
quantum chemical level. Goal of this project is the development of a fully
automated on-the-fly quantum mechanical/molecular mechanical (QM/MM) docking
approach and its application to the drug design for anti-cancer targets,
which will be evaluated in the translational research environment of the 
Medical Oncology Center in Lausanne.

We are seeking a highly motivated PhD student with a background in
(theoretical and organic) chemistry, (bio-) physics, or related disciplines
who is willing to work with a multi-disciplinary team. Basic programming
skills and proficiency in spoken and written English are prerequisites.
Starting date is negotiable.

The Swiss Institute of Bioinformatics in Lausanne provides a stimulating and
international environment as well as state-of-the-art computing facilities
and infrastructure. For more information see
Candidates should send a letter of motivation, a CV, contact details of two
referees, and a brief statement of research experience electronically to
Vincent Zoete ( and Ute Roehrig

Chemo-informatician Job

Drug Discovery Centre at the Paterson Institute is presently seeking an enthusiastic and proactive Informatician, on a 1-year fixed-term contract, to support, develop and expand the group's pre-existing capabilities in chemo- and bioinformatics.
The Drug Discovery Unit forms part of the Paterson Institute, one of Europe's premier cancer research centres. The Institute supports numerous basic and translational cancer research programmes facilitated by a comprehensive range of state-of-the-art research services (see: and is ideally sited next to The Christie, Europe's biggest specialist cancer hospital. The Institute lies at the heart of the Manchester Cancer Research Centre (MCRC), an exciting development that integrates cancer research within Manchester ( Details of the Unit itself can be found at
Qualified at least to BSc level in a chemical or biological discipline, or with appropriate equivalent experience, the successful candidate will have demonstrable experience in chemical and biological database administration, management and customisation within an Oracle environment. Experience in HTML and SQL would also be advantageous. Specific experience of informatics within a drug discovery environment and/or familiarity with the Dotmatics informatics platform is also highly desirable, perhaps gained through industrial experience. Additional familiarity with other chemo- and bioinformatics tools such as Pipeline Pilot, KNIME and Oncomine would also be desirable.
Informal enquiries should be addressed to Dr Allan Jordan, Head of Chemistry ( )
To apply for this position please visit our website:
For applicants who are unable to download this information from our website, please contact HR department on 0161 446 3231, email: to have this information sent by post.
The deadline for receipt of applications is 17th October 2011.

PhD positions at EPFL, Switzerland

Computational/theoretical chemistry PhD positions are available starting January 2012 
in the Laboratory for Computational Molecular Design at the Swiss Federal Institute of 
Technology (EPFL, Lausanne). The annual salaries are roughly 50,000 CHF. 

Our laboratory is interested in the development and application of accurate electronic 
structures approaches for rationally designing pi-conjugated molecules and materials. 

For detailed information on the projects, interested candidates are encouraged to 
contact Clemence Corminboeuf by email at 
and include a CV, a brief description of research interests, as well as 2 references. 
Prospective candidates should have finished their undergraduate studies and have some
background in theoretical/computational chemistry or physics. 
Knowledge of Linux-/Unix-based computer systems and Fortran programming languages 
would be an asset. 

These positions require acceptance in the doctoral program of Chemistry and Chemical 
Engineering, for which you may file an application at:
  contact Clemence Corminboeuf by email at

Computational Science Ph.D. program

Applications are invited for a tenure-track assistant or associate 
professor in the new Computational Science Ph.D. program. Applicants 
should have a strong potential to obtain external funding and to become 
excellent researchers and teachers at MTSU. Successful candidate must be 
interested in working with students in the Computational Science Ph.D. 
program. Research in data intensive science (biological data, remote 
sensing, astro-informatics, scientific applications of computer vision, 
for example) is preferred, although areas of Computational Science will 
receive full consideration. 
Position starts August 1, 2012. 
Minimum Requirements: Ph.D. in Biology, Chemistry, Computer Science, Mathematics, 
Physics or Computational Science, research in an area of computational 
science with a strong potential for funding. 
Preferred Requirements: 
Experience mentoring Ph.D. students and teaching, strong publication 
record; proven record of obtaining research funding, experience working 
in an interdisciplinary environment. 
Apply at 
If you have questions, please contact Dr. John Wallin, Director, at 
615-494-7735 or jwallin** EO/AA Employer.

Monday, 19 September 2011

QM/MM and QM Studies and Modeling of Heme and Nonheme Enzymatic Reactivity and Structure, and Brain Chemistry

Research Site:
The Institute of Chemistry and the Lise Meitner Minerva Center for 
Computational Quantum Chemistry, The Hebrew University of Jerusalem,
 Jerusalem, Israel

See for example the following papers:
(1) Shaik, S. Cohen, Y. Wang, H. Chen, D. Kumar, and W. Thiel
P450 Enzymes: Their Structure, Reactivity and Selectivity, Modeled by 
QM/MM Calculations
Chem. Rev. 110, 949-1017 (2010).
(2) S. Shaik, W.Z. Lai, H. Chen, Y. Wang
The Valence Bond Way: Reactivity Patterns of Cytochrome P450 Enzymes and
 Synthetic Analogs
Acc. Chem. Res. 43, 1154-1165 (2010).
(3) S. Shaik
Iron Opens to High Reactivity
Nature Chem. 2, 347-348 (2010).
(4) S. Shaik, H. Chen, D. Janardanan
Exchange-Enhanced Reactivity: A General Concept in Bond Activation by 
Metal-Oxo Enzymes and Synthetic Reagents
Nature Chem. 3, 19-27 (2011).
(5) H. Chen, W.Z. Lai, S.  Shaik
A Review on: Multireference and Multiconfiguration Ab Initio methods in
 Heme Related Systems: What Have We Learned So Far?.
J. Phys. Chem. B. 115, 1727-1742 (2011)

The candidate will participate in a project involving molecular dynamics
simulations, QM/MM and QM calculations of the highly active species of 
these enzymes. The applied techniques are described in the above papers
(see e.g., Ref. 1, above). In addition the candidate will participate in
 modeling and understanding the reactivity patterns (see Ref. 2 and 4
 above) Therefore, the candidate should have capabilities necessary to 
the computational methods and solid knowledge of quantum chemistry in
 order to do the modeling.

Candidate's profile:
The fellowship is designated for holders of Ph.D. in Chemistry 
(Theoretical Chemistry), Physics or a similar discipline, with curriculum
 adequate for the work described above. 

The candidate will be chosen based on the following criteria:
 The theoretical expertise gained during the Ph.D. or a previous postdoc 
research.  Important qualifications are: Expertise in applications of 
quantum chemical methods (DFT and Multireference or highly correlated ones)
, molecular dynamics methods, programming skills are good to have but not
 absolutely necessary.

 Indicators of scientific production, such as publications, conference
 presentations, books etc.
 Command of the English language

Extendible up to 4 years upon mutual consent.

The fellowship is paid according to the indices of the Hebrew University 
(5,600 IS/month + 150 USDA/month of housing support) and is tax free.

Required documents:
 Motivation letter, and a one-two page(s) research proposal.
 Curriculum vitae and list of publications
 3 letters of recommendation

a committee including the research Director, Prof. Sason Shaik, will 
evaluate the applications.

The applications should be submitted until October 7th, 2011. However, 
the deadline is extendable.
  Address for application submission:

Professor Sason Shaik, Director
The Lise Meitner-Minerva  Center for Computational Quantum Chemistry, 
Institute of Chemistry 
The Hebrew University of Jerusalem, Givat Ram Campus, 
Jerusalem 91904, ISRAEL
FAX: +972-2-6584680
Phone: +972-2-6585909

Computational protein engineering

Immediate openings of two postdoctoral research associates
interested in one or more of the following topics: 
1) drug resistance mutations in proteins;
2) computational engineering of protein stability;
3) protein unfolded states;
4) protein and RNA electrostatics 

- highly motivated individual holding a PhD in chemistry, chemical
  engineering, physics or a related field
- experience with one of molecular dynamics simulation packages such as
- programming and scripting skills
- good oral and written English language skills

We offer:
- training in the development and/or application of state-of-the-art
  molecular simulation techniques
- salary is commensurate with experience in the range of $34-40k/yr
- fun and flexible work environment
- one-year contract extendable up to three years upon mutual agreement

See for details of the group research interests

Norman is a safe and low-cost college town close to Oklahoma City. In
2006, it was voted by CNN Money as one of the 50 best places in the US
to live. Contact Dr. Shen for more info on location.
Please email CV in PDF format and the names of two reference persons to
Dr. Jana Shen
Department of Chemistry and Biochemistry
University of Oklahoma
Norman, OK 73019

Computation Studies of Aqueous and Ionic Liquids Interfaces

Postdoctoral Position: Molecular Theory Group at the Pacific Northwest 
National Laboratory has a postdoctoral position available immediately. 
Research interests will be focused on the development of classical and 
quantum statistical mechanical approaches to the study of bulk nanofluids 
and interfaces.
Interested applicants should send resume along with two 
letters of recommendation to Liem X. Dang (, 
Chemical & Materials Sciences Division, Pacific Northwest National 
Laboratory, P.O. Box 999, Mail Stop K1-83, Richland, WA 99352

Postdoctoral position in biomolecular simulation at Temple University, Philadelphia, PA

Lab is developing new computational methods to design folding and binding properties of
proteins and peptide mimetics.  Projects include: (1) developing Markov State Model (MSM)
approaches for modeling the folding reaction and designing sequences for folding properties
(2) simulation-based prediction and design of non-biological (e.g. peptoid) foldamers
(3) multiscale fragment-based approaches for predicting binding affinities and specificities of
protein-peptide interactions.   

Our lab benefits greatly from high-performance computing resources and collaborations available
through the Institute for Computational Molecular Science  (,
and inter-disciplinary collaborations through the new Moulder Center for Drug Discovery in the
School of Pharmacy.

More information at

Applicant should have a Ph.D in computational/physical chemistry, biophysics, chemical
engineering, or related field, and a strong background in molecular simulation, physical
chemistry, statistical mechanics of biomolecular systems, and/or computational biophysics.
Relevant research experience may include:  conformational sampling using molecular dynamics
or Monte Carlo simulation, free energy estimation, methods for estimating protein-ligand
affinities, protein structure prediction, forcefield development, multiscale modeling.

Good programming skills are essential, as the applicant will be responsible for writing new
simulation algorithms and extending existing code bases.  Other relevant skills include:
familiarity with simulation/modeling packages such as AMBER, GROMACS, OpenMM; Python
scripting experience; familiarity with UNIX; experience with large-scale scientific computing.
Experience with parallel computing and/or GPUs a plus.

Start date: negotiable (early 2012)
Salary: Competitive and commensurate with experience.
One-year appointment, with the option to extend contingent on satisfactory progress.
To apply:  Email a cover letter and your full CV (details of all academic degrees obtained, research
skills and experience, publications, conference presentations) preferrably as a single PDF, along
with 2-3 letters of recommendation, to Prof. Vincent Voelz

MD free energy calculations, Univ. of New Orleans, LA

Seeking a postdoctoral candidate with experience in molecular simulations or molecular modeling 
to work on an exciting research project at the interface of chemistry, physics and biology. 
The research focuses on extending and applying molecular dynamics-based free energy methods 
for predicting binding between small molecules (such as potential pharmaceutical drugs) and 
protein receptors. For reference, see my published work in this area. An ideal candidate would have 
substantial background in molecular modeling, ideally including molecular dynamics simulations 
and/or Monte Carlo, including applications and methodology work. Experience with free energy 
techniques is also a plus. 

Interested applicants should send a cover letter plus a CV to Additionally, 
please have at least three letters of reference sent to the same address as well. All application 
materials should be received by Oct. 21, 2011. Prospective applicants are welcome to contact 
me for more information. The position will likely start in January, 2012. 

The University of New Orleans, and the New Orleans area, provide exciting opportunities for work 
in this area. In addition to the Mobley Lab at UNO, we maintain close contacts with Steve Rick's 
group, also in Chemistry at UNO, and Chris Summa's group in computer science. Both labs have
 interests in molecular simulations, free energy calculations, and statistical mechanics. We also
interact with the groups of Hank Ashbaugh and Lawrence Pratt at Tulane University, as well as 
various experimental and computational collaborators worldwide.

Thank you so much.
David Mobley
Department of Chemistry
University of New Orleans

Tuesday, 6 September 2011

Computational Chemistry, Rouen University, France

Our strategy: a quantum chemical approach in three major steps :

The analysis of the electronic properties of selected molecular systems requires a quantum
chemical approach. As a first step, we need to validate the method, comparing simulated fluorescence
spectra of already synthesized molecules with experimental ones. In order to avoid time-consuming
calculations, we decided to base all our calculations on density functional theory (DFT), a method of
choice for our problem. In particular, the time-dependent DFT (TDDFT) method produces an
accurate description of excited states, comparable to DFT for the ground state. On the other side,
Franck-Condon and Herzberg-Teller analyses can be used for computing the amplitudes for electronic
transitions from the ground and excited state frequency analyses. For instance, the combination of the
two have been recently employed with success to compute the Herzberg-Teller absorption and
fluorescence spectra of free-base porphyrins.8 It is interesting to mention that solvent effects can be
taken into account.

As a second step, we need to understand the reasons leading to the observed differences in
fluorescence activity between our selected analogues. Different approaches will be envisaged such as
orbital analyses or topological studies of the electron density, both in fundamental and excited states.
Concerning the topological approach, based on the quantum theory of atoms in Molecules (QTAIM),
excited state properties are yet completely unexplored, constituting a real challenge in this field of
quantum chemistry. This information could be of the prime importance to design the next generation
of epicocconone analogues.

In the final step, our validated approach will be used to predict fluorescence properties of the
newly designed series of analogues, guiding experimentalists for new syntheses.

Possible additional tasks:

1) Reactivity studies:
Mechanisms of some steps involved in the synthesis of these fluorophores, not only from a static 
viewpoint (transition states), but also dynamical. To this aim, the PW-GTO-mixed CP2K code could 
be used to carry out Born-Oppenheimer dynamical simulations. The exploration of these complex 
energy surfaces could be done through a metadynamics approach as pioneered by Laio and Parrinello. 
This method could also provide efficient way of evaluating entropy in solution (cf. Michel and Laio), 
and thus Gibbs energies, enabling a realistic description of the reactivity of such species. 

2)Theoretical developments: 
- new reactivity descriptors within the framework of conceptual DFT 
(from Morells dual descriptor) and QTAIM, applied to fluorescence problems. We are 
currently developping our own parallel code for topological analyses 
- new parameter to quantify the accuracy of TDDFT calculations (for instance, assesment 
and improvement of Tozers  parameter)
-  PCM solvent model and excited states
- implementation and design of fully non-local correlation functionals for van der Waals
interactions (such as Lundqvist, van Voorhis ones)

Additional information :

Salary : 1850 euros / month (contract for 12 months)

How to apply ? Please contact Prof. laurent Joubert:
sending a detailed CV and explaining your motivation for this position.

Laboratory : IRCOF, University of Rouen, France. Group of theoretical chemistry