Macs in Chemistry

Insanely Great Science

ChemDraw Innovation Challenge

 

Perkin-Elmer have just announced the ChemDraw Innovation Challenge - a forum designed to shape the future of Chemdraw

For the past 30 years, ChemDraw has been known around globe as the premier chemical drawing tool for chemists and biologists alike. While each version has brought more powerful features (many of which came from feedback from our passionate user base), we’ve all had that moment where we wanted ChemDraw to do [X]. We want to hear your ideas, suggestions for new features, new third-party applications we should integrate and more. The sky's the limit - big or small, all ideas are welcome!


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A question on Network storage devices

 

I'm running out of storage space on my Synology NAS and I"m thinking of adding another device.

Current options are an updated 2 bay device Synology DS213J 10TB (2 x 5TB) 2 Bay Desktop Network Attached Storage which can accommodate upto 10TB of storage. Alternatively I could go for the 4-bay device Synology DS416 12TB (4 x 3TB WD RED) 4 Bay Desktop NAS which offers greater capacity, or similar capacity with 4 smaller drives.

Any views on the reliability of the larger capacity HDDs ?


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HP says 3D printing is moving from niche to production

 

The 3D printing page always attracts a regular stream of readers so I thought I'd flag this article from HP.

Digital manufacturing with 3D printing has the potential to disrupt the $12 trillion global manufacturing sector, said Timothy Weber, HP vice president and general manager of 3D materials and advanced applications.

HP began shipping its model 4200 Multi Jet Fusion units with Voxel-level 3D printing, that has a 21-micron resolution.


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A webinar demonstrating using Jupyter, the free iPython notebook

 

This is a recording of the March 2017 Global Health Compound Design meeting. A webinar demonstrating using Jupyter, the free iPython notebook.

https://youtu.be/XqyWctQxhNs

How to get started

Accessing Open Source Malaria data

Calculating physicochemical properties and plotting

Predicting AMES activity.



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ORCA 4.0 released

 

The latest update to ORCA has just been released.

The program ORCA is a modern electronic structure program package written by F. Neese, with contributions from many current and former coworkers and several collaborating groups. The binaries of ORCA are available free of charge for academic users for a variety of platforms. ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. Due to the user-friendly style, ORCA is considered to be a helpful tool not only for computational chemists, but also for chemists, physicists and biologists that are interested in developing the full information content of their experimental data with help of calculations.

New Features of Version 4.0:

New Methods:

  • Linear scaling DLPNO-CCSD(T) open shell. New restricted open-shell formulation
  • Linear scaling DLPNO-MP2 (RHF and UHF)
  • Linear scaling DLPNO-MP2-F12 (RHF)
  • Linear scaling DLPNO-CCSD(T) (the 2013 implementation is still available)
  • Linear scaling DLPNO-CCSD(T) local energy decomposition scheme
  • Linear scaling DLPNO-CCSD closed shell density
  • Linear scaling cluster in molecule (CIM): MP2, CCSD(T), DLPNO-CCSD(T)
  • Linear scaling DLPNO-NEVPT2
  • NEVPT2-F12
  • Updated interface to BLOCK 1.0
  • DMRG-NEVPT2
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Partial PNO-EOM-CCSD method for excited states
  • Partial PNO-STEOM-CCSD method for excited states
  • DLPNO-CCSD-F12, LPNO-CCSD-F12
  • Mukherjee Mk-LPNO-MRCCSD(T)
  • Powerful iterative configuration expansion (ICE-CI) approximation to Full-CI
  • ICE-CI for large active space CASSCF calculations
  • MREOM-CCSD (also with SOC)
  • Fully internally contracted MRCI
  • Full TD-DFT energies and gradient for hybrid functionals
  • Super-fast approximate TD-DFT: sTDA/sTDDFT of Grimme and co-workers
  • PBEh-3c method of Grimme and co-workers

SCF, DFT and Hessian:

  • Large performance improvements for calculations with four center integrals
  • Improved performance with RI-J with conventionally stored integrals
  • Gradient for range separated hybrids
  • Gradient for range double hybrid functionals with meta GGAs
  • Gradient for range double hybrid functionals with range separated functionals
  • Gradient for RI-JK
  • Frequencies for range separated functionals
  • Stability analysis and automatic search for broken symmetry states
  • Local spin analysis
  • Fractional occupation number analysis (FOD) for detection of MR character

MDCI module:

  • All improvements for DLPNO methods as listed above
  • Closed shell EOM-CCSD energies
  • Closed shell STEOM-CCSD energies
  • Automatic closed shell STEOM-CCSD active space selection
  • EOM-CCSD(2) and STEOM-CCSD(2) approximations
  • EOM-CCSD transition moments
  • EOM/STEOM-CCSD core level excited states
  • IP-EOM-CCSD and EA-EOM-CCSD
  • ADC(2) and CC(2) methods (initial implementation)
  • COSX for EOM-CCSD and STEOM-CCSD
  • Improved automatic frozen core handling
  • Core-correlation in automatic basis set extrapolation

AUTOCI module:

  • RHF/UHF CISD
  • RHF/UHF CCSD
  • ROHF CISD
  • ROHF CCSD
  • FIC-MRCI, CEPA/0 variant and DDCI3

CASSCF, NEVPT2 and MRCI

  • Detailed tutorial showing CASSCF/NEVPT2 usage
  • Accelerated CI (ACCCI) a more efficient CI step for multi-root calculations
  • Automatic implementation of AbInitio ligand-field theory
  • Simplified generation of double-shell orbitals
  • Active space protection scheme and improved warnings
  • ICE-CI as CI solver for larger active spaces
  • Partially Contracted NEVPT2 with and without RI
  • Updated interface to BLOCK 1.0
  • DMRG-NEVPT2 for active spaces up to 20 orbitals
  • Magnetization and magnetic susceptibility
  • Printing of the wavefunction in terms of CSFs and spin-determinants
  • MREOM-CCSD (also with SOC)
  • Local spin analysis for CASSCF
  • Fragment decomposition of the spin-spin interaction
  • Cumulant approximation for NEVPT2
  • ACCCI as CIStep for FIC and DLPNO-NEVPT2
  • Explicitly correlated RI-FIC-NEVPT2 (NEVPT2-F12)

TD-DFT and ROCIS:

  • Full TD-DFT for hybrid functionals
  • Gradient for full TD-DFT with hybrid functionals
  • TD-DFT/TDA gradient with range separated functionals
  • ROCIS magnetic properties (hyperfine, g-tensor, ZFS tensor, MCD)
  • ROCIS-RIXS spectra
  • PNO-ROCIS for spectacular performance improvements
  • Super-fast approximate TD-DFT: sTDA/sTDDFT
  • Natural transition orbitals in TD-DFT and ROCIS

Miscellaneous:

  • GIAO implementation for NMR chemical shifts. Various aproximations (RIJOCOSX, RIJK)
  • New Handling of basis set names. Now fully consistent with TurboMole def2-defaults (including ECPs) SARC basis sets separately available
  • New reading of basis sets and ECPs together
  • New correlation consistent basis sets added
  • New SARC basis sets for the lanthanides; good for correlated calculations
  • New ANO-RCC basis sets added
  • Improved frozen core handling in correlation calculations
  • Improved automatic auxiliary basis set generation
  • Corrections for low-frequency modes in thermochemistry
  • New and improved NBO interface
  • CPCM and improved SMD solvent models
  • Intrinsic atomic orbital (IAO) and bond orbital implementation
  • Improved performance in Boys localization
  • Updated and improved mapspc program
  • Atomic Mean Field (AMFI) spin-orbit coupling operators
  • EPRNMR works with range separated hybrid functionals
  • New molecular dynamics module

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