"Released in July by Cranbury, N.J.-based Millsian, Inc., Millsian v2.0 Beta is a 3-D molecular visualization program that can calculate the physical characteristics of structures of almost any size or complexity. Chemists can use the software to build structures or import them from databases; it handles and converts between SMILES, MOL, and PDB file formats. Large imported structures such as those of proteins or DNA fragments can be edited and corrected for missing hydrogens or miscalculated bond orders. Users can further evaluate binding pockets and reactive sites in structures with the help of analytically calculated whole-molecule charge distribution profiles. In addition, they can compute dipole moments and rotational barriers for molecular conformation changes."

Millsian 2.0: A Molecular Modeling Software for Structures, Charge Distributions and Energetics of Biomolecules - W. Xie, R.L. Mills, W. Good, A. Makwana, B. Holverstott, N. Hogle

In this molecular modeling paper, we provide the methods and algorithms that utilize Mills classical physics atomic and molecular solutions in the molecular modeling software package called Millsian 2.0 designed for modeling the 3D structures, charge distribution, and energetics of biomolecules of pharmaceutical interest. The implementation of Millsian 2.0 was extensively tested against the available experimental data with remarkable agreement between Millsian predictions and experiments.

Total Bond Energies of Exact Classical Solutions of Molecules Generated by Millsian 1.0 Compared to Those Computed Using Modern 3-21G and 6-31G* Basis Sets - R.L. Mills, B. Holverstott, W. Good, N. Hogle, A. Makwana

Summary: In a new molecular modeling paper, the energies of exact classical solutions of molecules generated by Millsian 1.0 and those from a modern quantum mechanics-based program, Spartan's pre-computed database use 3-21G and 6-31G* basis sets at the Hartree-Fock level of theory, were compared to experimental values. The Millsian results were consistently within an average relative deviation of about 0.1% of the experimental values. In contrast, the 3-21G and 6-31G* results deviated over a wide range of relative error, typically being >30-150% with a large percentage of catastrophic failures, depending on functional group type and basis set.

Molecules page updated with new renderings of molecules using exact charge distribution profiles.

New animation of the Bound Complex and Transition State of Cl- CH3Cl.

Software page updated with Millsian 2.0 features.

New animations: DNA and Insulin rendered for the first time ever with exact charge distribution profiles.

(Chp 9) Figure of analytical solutions of the excited states of helium.

(Chp 12) Figure of analytical solutions of the excited states of molecular hydrogen based on prior classical solutions released in December '08.

(Chp 15) Figures of analytical solutions of bovine pancreatic trypsin inhibitor (BPTI) protein and a double-stranded DNA helix created and modeled using Millsian 2.0 showing true charge density which was not previously possible even using supercomputers.

(Chp 16) (i) bond moments of major set of functional groups that give the charge distribution within an unlimited number of molecules as well as the resulting molecular dipole moments with exemplary rendering of analytical solutions of insulin, lysozyme, and a double-stranded DNA helix using Millsian 2.0 showing true charge density which was not previously possible even using supercomputers; (ii) nature of the dipole bond which is the basis of dipole-dipole, hydrogen, and van der Waals bonding and molecular interactions; (iii) condensed matter physics based on first principles; (iv) analytical solutions of the geometrical parameters and energies of the hydrogen bond of H2O in the ice and steam phases, and of H2O and NH3; (v) analytical solutions of the geometrical parameters and interplane van der Waals cohesive energy of graphite; (vi) analytical solutions of the geometrical parameters and interatomic van der Waals cohesive energy of liquid helium and solid neon, argon, krypton, and xenon; (vii) classical theory of reaction kinetics and thermodynamics; (viii) classical transition state theory with analytical solutions that match data extraordinarily well replacing tasks that are very challenging even using supercomputers involving algorithms having many adjustable parameters; the same applies for water, graphite, and condensed noble gasses of topics (iv-vi).

Updated Summary Tables including molecules solved by Millsian compared to experimental values.

Partial List of Organic Functional Groups Solved by Classical Physics

Partial List of Additional Molecules and Compositions of Matter Solved by Classical Physics

Spreadsheets for (i) bond moments of major set of functional groups; (ii) analytical solutions of the geometrical parameters and energies of the hydrogen bond of H2O in the ice and steam phases, and of H2O and NH3; (iii) analytical solutions of the geometrical parameters and interplane van der Waals cohesive energy of graphite; (iv) analytical solutions of the geometrical parameters and interatomic van der Waals cohesive energy of liquid helium and solid neon, argon, krypton, and xenon; (v) analytical solutions of the C complex and transition state of the reaction of chloride ion with chloromethane.

Reaction Mechanism-Animation of the reaction of chloride ion with chloromethane based on analytical solutions of the C complex and transition state.

Powerpoint Update of Theory Presentation Part 2:
(This is a large file which may take a while to load.)
(i) figures of analytical solutions of the excited states of helium, molecular hydrogen, proteins, DNA and RNA; (ii) bond moments of major set of functional groups; (iii) analytical solutions of the geometrical parameters and energies of the hydrogen bond of H2O in the ice and steam phases, and of H2O and NH3; (iv) analytical solutions of the geometrical parameters and interplane van der Waals cohesive energy of graphite; (v) analytical solutions of the geometrical parameters and interatomic van der Waals cohesive energy of liquid helium and solid neon, argon, krypton, and xenon; (vi) transition state theory and analytical solutions of the C complex and transition state of the reaction of chloride ion with chloromethane.

The June 2008 Edition of Dr. Mills' Book is now available. The October 2007 Edition is available to buy.

Summary of updates: Nonradiation derivations were consolidated in Appendix I, and the Introduction and Chapter 1 were edited to give the boundary-value derivation of the structure of the electron comprising an invariant, time-varying, electromagnetic source current and further giving the relationship to the 2-D wave equation. The prior approach of bridging the new classical theory with the historical wave equation was dropped. The Foreword was dropped reflecting a textbook format. The Preface was updated.

Other new topics solved in this edition are:

• Chapter 15: Amino acids and peptide bonds with charged functional groups for proteins of any size and complexity, bases, 2-deoxyribose, ribose, phosphate backbone with charged functional groups for DNA of any size and complexity, organic ions, halobenzenes, phosphines, phosphates, phospine oxides, phospates.
• Chapter 23: Organogermanium and digermanium, organolead, organoarsenic, organoantimony, organobismuth.
• Chapter 42: Wheeler's delayed-choice gedanken experiment.

1/19/08

7/27/07

Interactive, exact solution and rendering of 15,000-carbon-atom polystyrene molecule (~150,000 daltons) has been performed by a PC in real time using the next generation Millsian software under development.

6/15/07

The beta-version of Millsian software is now available for download. Users may use the software for free for a 14-day trial period.

This version of the software includes recently solved molecules including silanes and alkyl silanes, organometallics, and boron containing molecules.