Cam

bridgeSoft SolutionsC

ambridgeSoft Solutions

ChemBioOffice 2008 Tips & Tricks

Webinar

Jesse Gordon

Biology Director

jgordon@cambridgesoft.com

(617) 588-9306

Skype: jessegordon

ChemBioOffice 2008 - The Desktop Productivity Toolkit for Scientists

ChemBioOffice

• Scientists Need Offices too!• ChemBioOffice is the

Desktop Standard for Research by Scientists

• ChemBioOffice provides the desktop tools scientists need, right at their fingertips

• ChemBioOffice integrates with Enterprise Solutions (such as the CambridgeSoft Enterprise and ELN suites) providing a Fully Integrated Scientific Management System that extends across the corporation

ChemBioOffice 2008 Applications - The Desktop Productivity Suite for Scientists

The ultimate chemistry & biology suite, designed to meet the needs of both chemists and biologists

• ChemBioDraw Ultra 11.0• ChemBio3D Ultra 11.0• ChemFinder/BioViz Ultra 11.0 with support for Oracle• MestReC Std • ChemScript Pro 11.0• ChemDraw/Excel 11.0• CombiChem/Excel 11.0• ChemDraw & Chem3D ActiveX Pro Plugins & Controls 11.0• ChemINDEX (Index, RXN, NCI & AIDS)• 1-year subscriptions to ChemACX and ePub

• BioAssay Ultra 11.0• Inventory Ultra 11.0 • E-Notebook Ultra 11.0

Now Vista and MS Office 2007 Compatible!

Now Vista and MS Office 2007 Compatible!

Chem

BioV

iz Ultra S

uite

ChemBioOffice Annual Site License

-Cost Effective Collaboration

• Unlimited usage within institution (hence lower cost per user)

• All departments have access to the specific software they need

• Software updates and administrator support included

• Software can be used on any machine (lab, laptop, home use)

• Individual online software download means less administration

• Site licenses reduce support load

• Multi-year site licenses reduce long-term cost

Work faster with ChemBioDraw 11.0

- You do more Research

• ChemDraw Ease of Use– Customizable Hot Keys, Templates, Nicknames

• New Chemistry Features– Sequence Tool– Structure Clean-up and Stereochemistry Enhancements– New Reaction Interpretation, SD file support , R-Group logic

• Improved Productivity and Application Integration– Customizable Themes and Preferences – LiveLink to Databases; Chem3D LiveLink

• Advanced Chemical Intelligence– Hotlinking, Property Predictions, Naming, ChemDraw/Excel

• New Drawing Features– Flexible Arrows– Freehand Pen Tool

• New BioDraw tools– Enhanced Illustration of Biological processes– Completely Integrated with ChemDraw– New Plasmid Map and other tools

• Extended Platform Support– Windows Vista– MSOffice 2007– Native support of Intel on Mac

S

R RR

R

New 11.0 Version

New 11.0 Version

Work faster with ChemDraw

- ChemDraw Reduces Drawing Time

Hotkey Result1 Change to single bond.

2 Change to double bond.

3 Change to triple bond.

4 Change to quadruple bond.

c Center a double bond.

l Position a double bond to the left.

f Bring a bond to the front.

a A

A or 5 Ac

b Br

Customizable Hotkeys

• Use Hotkeys to draw chemical structures in less than half the time

• Avoid going back to the Tools Palette to change tools - those mouse motions and clicks add up to a lot of extra time!

• Share Hotkey customizations with colleagues

Complex structures take seconds to draw vs.

minutes

• Save hours by using predefined rings, templates and drawings

• Create custom templates, reducing time for repeated experiments

Customizable Templates

Work faster with ChemDraw

- ChemDraw Reduces Drawing Time

Improved Access in v11

Improved Access in v11

Reduce Document Clutter

- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full

detail, but instead are represented by a chemically intelligent label that can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

Improved in v11

Improved in v11

Reduce Document Clutter

- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full detail,

but instead are represented by a chemically intelligent label that can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

Improved in v11

Improved in v11

Reduce Document Clutter

- Communicate key chemistry more effectively

Customizable Nicknames

• Simplify and speed up chemical drawings using Nicknames• Draw structures where parts of the molecule aren’t shown in full detail,

but instead are represented by a chemically intelligent label that can be expanded and contracted

• Define new nicknames in ChemDraw to fit your research

Improved in v11

Improved in v11

New Sequence tool - Easily Create Amino Acid, DNA, RNA sequences

• Draw peptide and nucleotide sequences

• Several modes:- Single-letter amino acid

tool- Three-letter amino acid

tool- DNA tool- RNA tool

• Termini are labeled depending on the type of sequence drawn

• Expand and contract single or multiple labels and sequences

New in v11

New in v11

C

NH

O

HS

H

A

HN

O

G

HN

O

OH

T

NH

O

OH

Highest Presentation Quality Graphics

- Instant Structure and Reaction Clean-up

H H

H

S

S S

S O

O

O

O

H O

O

OHH

• One click with Structure or Reaction Cleanup provides neater, more accurate drawings

• Compare to multiple undo’s and adjustments to the structure – significant time savings

• Fixed Lengths and Fixed Angles options• Major Improvements to algorithm in version 11 supports a wide

spectrum of structure types

Improved in v11

Improved in v11

Positioning of hashed and

wedged bonds

Selection of base ring in cyclic system

Vertically oriented

carbonylsRemoval of overlap: Bridged rings

Advanced Drawing Conventions - Stereochemistry enhancements

• ChemDraw 11 has been enhanced to recognize the common drawing styles that represent tetrahedral stereochemistry without using stereo bonds in their usual sense

• Changes are consistent with the latest IUPAC recommendations for the depiction of stereochemistry

• Examples:

SR

SOR

S

HO

HOOH

OHOH

New in v11

New in v11

S

R RR

OR

HOHO

OHOH

OH

CHOR

S

OHH

R

HHO

R

OHH

CH2OH

OHH

(R)

OH

OH

ChemDraw Predicts Chemical Properties

– Make sure you are drawing what you expect

• Structural Analyses (Updated real-time)– Formula– Exact mass– Molecular Weight– Isotope distribution patterns– Elemental Analysis

• Physical Properties– Boiling Point– Melting Point – Critical Temp, Pres, Vol– Gibbs Energy– LogP– MR– Henry’s Law– Heat of Formation– CLogP– CMR

*Topoplogical Polar Surface, tPSA was added to the Chemical Properties in version 9.0

Improved in v11

Improved in v11

• “View 3D Preview” is a new menu item under the View menu

• A separate floating window shows a 3D model of the current structure as generated by Chem3D

• A current version of Chem3D must be installed

Chem3D HotLink - Integrated structural visualization

New in v11

New in v11

Database Gateway HotLink - Search structural databases in real time

• Real-time search– Search as you draw– Search all CS databases– Search internal databases

• Drill-down results– Click on data source name

to see results from that source

– Links open in external browser window so work in ChemDraw can continue

New in v11

New in v11

ChemDraw NMR Prediction

– Helps confirm Chemical Structures

• 1H NMR includes splitting Patterns

• Calculate predicted 13C NMR spectrum

Improved accuracy in v11

Improved accuracy in v11

ChemDraw NMR Prediction

– Helps confirm Chemical Structures

• 1H NMR includes splitting Patterns

• Calculate predicted 13C NMR spectrum

0123456PPM

Improved accuracy in v11

Improved accuracy in v11

MestReC Std processes 1D NMR Spectra

- Chemists can analyze their results in seconds

Data Format Vendor Dimensions

VXR/Unity/Inova Varian 1D **

Gemini/VXR Varian 1D

XWIN-

NMR/UXNNMRBruker 1D **

Aspect 2000/3000

Bruker 1D

Win-NMR Bruker 1D

JEOL GX/EX JEOL 1D

CDFF Nuts AcomNMR 1D **

JCAMP-DX 5.0 IUPAC 1D

NTNMr Tecmag 1DSwaN-MR Menarini 1D

SIEMENS NMR Siemens 1D

SIEMENS NMR Nicolet/GE 1D New in v10

New in v10

BaselineCorrection

PhaseCorrection

Analysis

MestReC Lite Import File Formats

• Basic NMR processing and analysis - ideal for multiple chemists running large numbers of routine experiments

• Compliments ChemDraw’s NMR prediction capabilities** Full version of MestReC also reads 2D in this format

Isotopes

Inner salts

Lambda convention

Name = Struct now handles more structure types and has a typo recognition feature

Instantly Generate Structures from Names

- Do more Lab work, less Drawing

Improved in v11

Improved in v11

Porphyrins

• Add chemical structures and other data from ChemDraw, MDL SDFiles or a ChemFinder database to an Excel spreadsheet

• Convert Names or SMILES Strings to Structures• Search using the same search features as ChemFinder• Perform calculations on chemical structures• Combinatorial Chemistry within Excel

- Automatic Generation of Product Lists

Chemical Intelligence within Excel

- Chemical calculations on Multiple Structures

ChemDraw/ExcelISSTRUCTUREISREACTIONCHEM.FORMULACHEM.MOLWEIGHTCHEM.NUM.HBAACCEPTORSCHEM.NUM.HBDONORSCHEM.SMILESCHEM.COMPOSITIONCHEM.NUM.ATOMS

Property FunctionLogP CHEMPROP.LOGPMolar Refractivity CHEMPROP.MRHenry’s Law Constant CHEMPROP.HENRY.LAW.CONSTANTBoiling Point CHEMPROP.BOILINGFreezing Temperature CHEMPROP.FREEZINGCritical Temperature CHEMPROP.CRITICAL.TEMPCritical Pressure CHEMPROP.CRITICAL.PRESSURECritical Volume CHEMPROP.CRITICAL.VOLUMEHeat of Formation CHEMPROP.HOFGibbs Free Energy CHEMROP.GIBBSIdeal Gas Thermal Capacity CHEMPROP.IDEAL.GAStPSA CHEMPROP.TPSA

Improved in v11

Improved in v11

Highest Presentation Quality Graphics

- Intuitive Freehand sketching tool

• The toolbar contains two items, “Draw Curve” (default) and “Edit Curve”

• Holding the “Shift” key reduces the amount of smoothness• The curves created can be further modified by selecting

and dragging control points

New in v11

New in v11

Highest Presentation Quality Graphics

- Adjustable Shapes, Arrows and more

• Arrow Types include: No-go, unbalanced equilibrium, dipole, multiple arrowheads

• Adjustable Arrows – Full control over arrow properties including Curves, color fill and shading - illustrate complex chemistry/biology mechanisms

• Rotatable and adjustable geometric shapes – rectangles and ovals

• Color-faded geometric shapes – rectangles and ovals

O

CH3

CH3H3C

SH SH

O

H3C

CH3H3C

SH SH

2,7,9-trimethyl-4aH -xanthene-4,5-dithiol

Improved in v11

Improved in v11

• BioDraw features are fully integrated into ChemBioDraw Ultra

• Use any BioDraw tool in any ChemDraw document

• Excellent collaborative tool

Integrate Chemistry and Biology Drawings - Facilitate Communication between Scientists

Expanded in v11

Expanded in v11

Integrate Chemistry and Biology Drawings - Facilitate Communication between Scientists

One or Two-substrate enzyme Receptor Ion Channel Helix Protein Linear membrane Arc membrane Golgi body Cloud G-Protein (alpha, beta or gamma subunit) ImmunoglobinDNA Micelle Ellipse membrane Endoplasmic Reticulum Mitochondrion

Draw Biological Pathways

Expanded in v11

Expanded in v11

BioDraw New Drawing tools

- Enhanced illustration of biological processes

• New tRNA Tool• New Ribosome Tool• New Plasmid Maps• DNA helix strands can

now be selected individually for modification

• Protein helix strands and cylinders can now be individually selected and modified

New in v11

New in v11

• Medicinal and cheminformatics groups can access high quality, easy to use visualization and computation tools at a low cost

• Visualize results from Computational Chemistry Group - assist in designing the next round of synthetic targets

• Protein and Nucleic Acid Ribbon Diagrams provide insight into tertiary and quaternary structure of proteins and protein complexes

Quality visualization on the Desktop - Structural insights, Team collaboration

ChemBio3D Ultra

ChemBio3D Extensions and API

- Gaussian and Jaguar Interfaces

Gaussian• Predict NMR, IR and Raman spectra • Support multi-step jobs and partial optimizations • New DFT tab • Monitor Gaussian Link processes

Jaguar• Surfaces: Total Charge Density surface, Total Spin

Density surface, Molecular Electrostatic Potential surface and Molecular Orbital surface

New in v10

New in v10

ChemFinder - Chemical Database Management System

• View and Build Your Own Chemical Databases• Create your own forms• Store chemical structures, physical properties, notes and tables of

data• Integrated with ChemDraw• Search data by

– Chemical structure (including sub-structure)– Wild card text searches– Numeric range searches

BioViz

Data visualization and analysis right in ChemFinderNo need to switch back and forth to other apps

Analyses are saved with the form

Get more out of your data

- Analysis right in ChemFinder with BioViz

Improved in v11

Improved in v11

Compound Profiles

- Compare structures based on Properties

Compound profilesVisually compare and rank structures based on values of selected properties and the cost profile associated with each property.

New in v11

New in v11

BioAssay, E-Notebook & Inventory

- Multi-user access with SQL Server 2005

• SQL Server 2005 Express - self tuning RDBMS• Support multiple users• Database limit now doubled - 4GB

For example: Inventory with 1000 compds + 1000 containers + 1000 MSDS 0.1 MB pdfs = 140 MB

• Supports Vista• Collaborative Workgroup Versions available

(SQL Server Std or Enterprise)

Cam

bridgeSoft SolutionsC

ambridgeSoft Solutions

ChemBioOffice 2008 Tips & Tricks

Webinar

Jesse Gordon

Biology Director

jgordon@cambridgesoft.com

(617) 588-9306

Skype: jessegordon