massXpert lets users analyse/predict mass spectrometric data on (bio)polymers. Notable features include ex nihilo polymer chemistry definitions, highly sophisticated editing of polymer sequences and chemical reaction simulations.

MAUD (Material Analysis Using Diffraction) is a general diffraction/reflectivity analysis program mainly based on the Rietveld method. It has a GUI, and a wide range of features including ab initio structure solution, various optimisation algorithms, Le Bail fitting and microstruture analysis.

Maxwell consists of a suite of programs that implement the Maxwellian formalism for calculating the interaction energy between charge distributions as represented by the multipole expansion. It can also be applied to crystal lattices.

MCCCS Towhee is a Monte Carlo molecular simulation code which can be used for the prediction of fluid phase equilibria using a wide variety of atom-based force fields and several ensembles (Gibbs, Canonical, Isobaric-isothermal and Grand Canonical). It has also been extended for use with solid (or porous) phases.

McMaille is a program for indexing powder diffraction patterns by Monte Carlo and grid search.

MCPRO performs Monte Carlo statistical mechanics simulations of peptides, proteins, and nucleic acids in solution; it was derived from BOSS, but makes extensive use of the concept of residues. Free energy changes can be computed via FEP calculations and have been used extensively for studying protein-ligand binding.

MCTDH (Multi Configuration Time Dependent Hartree) is a general algorithm to solve the time-dependent Schrödinger equation for multidimensional dynamical systems consisting of distinguishable particles. MCTDH can thus determine the quantal motion of the nuclei of a molecular system evolving on one or several coupled electronic potential energy surfaces. MCTDH can also be used to propagate density operators and to determine eigenvalues and eigenstates of a molecular vibrational Hamiltonian.

MDTools is a collection of programs, scripts, and utilities to make various molecular dynamics tasks easier, and to provide basic code and utilities which can be built up into larger toolsets.

Mercury is a program for visualising crystal structures in three dimensions. Its features include:The ability to load hit lists from ConQuest searches, or to browse the entire Cambridge Structural Database, or to read in crystal structures in various formats. The ability to rotate and translate the 3D crystal-structure display, and to view down cell axes, reciprocal cell axes, and the normals to least-squares and Miller planes. The ability to measure and display distances, angles and torsion angles by atom picking and much more.

MeTA Studio is programmable IDE tailored for a computational chemist. It has support for BeanShell and Jython, and integrates Jmol.