diff --git a/Examples.md b/Examples.md
index 4cf749f9..ff050b81 100644
--- a/Examples.md
+++ b/Examples.md
@@ -1,4 +1,5 @@
-  - [Sample input files](Sample)
+# EXamples
 
+## [Sample input files](Sample.md)
 
-  - [Examples of geometries using symmetry](Geometry-examples)
+## [Examples of geometries using symmetry](Geometry-examples.md)
diff --git a/Hybrid-Approaches.md b/Hybrid-Approaches.md
index be703976..1b185755 100644
--- a/Hybrid-Approaches.md
+++ b/Hybrid-Approaches.md
@@ -1,25 +1,15 @@
-  - [COSMO Solvation Model](COSMO-Solvation-Model)
+# Hybrid Approaches
 
-<!-- end list -->
+## [COSMO Solvation Model](COSMO-Solvation-Model.md)
 
-  - [SMD Model](SMD-Model)
+## [SMD Model](SMD-Model.md)
 
-<!-- end list -->
+## [VEM Model](VEM-Model.md)
 
-  - [VEM Model](VEM-Model)
+## [Hybrid Calculations with ONIOM](ONIOM.md)
 
-<!-- end list -->
+## [Combined quantum and molecular mechanics (QM/MM)](QMMM.md)
 
-  - [Hybrid Calculations with ONIOM](ONIOM)
+## [External charges (Bq)](Bq.md)
 
-<!-- end list -->
-
-  - [Combined quantum and molecular mechanics (QM/MM)](QMMM)
-
-<!-- end list -->
-
-  - [External charges (Bq)](Bq)
-
-<!-- end list -->
-
-  - [1D-RISM ](1D-RISM)
+## [1D-RISM ](1D-RISM.md)
diff --git a/Other-Capabilities.md b/Other-Capabilities.md
index c8ed229c..fc664aa2 100644
--- a/Other-Capabilities.md
+++ b/Other-Capabilities.md
@@ -1,7 +1,15 @@
-  - [Electron Transfer Calculations](Electron-Transfer)
-  - [Controlling NWChem with Python](Python)
-  - [Quantum Computing](Quantum)
-  - [VSCF](VSCF)
-  - [Dynamical Nucleation Theory Monte Carlo](DNTMC)
-  - [Correlation consistent Composite Approach (ccCA)](CCCA_method)
-  - [Interfaces to Other Programs](Interface)
+# Other Capabilities
+
+## [Electron Transfer Calculations](Electron-Transfer.md)
+
+## [Controlling NWChem with Python](Python.md)
+
+## [Quantum Computing](Quantum.md)
+
+## [VSCF](VSCF.md)
+
+## [Dynamical Nucleation Theory Monte Carlo](DNTMC.md)
+
+## [Correlation consistent Composite Approach (ccCA)](CCCA_method.md)
+
+## [Interfaces to Other Programs](Interface.md)
diff --git a/Quantum-Mechanical-Methods.md b/Quantum-Mechanical-Methods.md
index 21e79b83..3d582c8d 100644
--- a/Quantum-Mechanical-Methods.md
+++ b/Quantum-Mechanical-Methods.md
@@ -1,43 +1,43 @@
 # Quantum Mechanical Methods
  
 
-## [Hartree-Fock (HF) Theory](Hartree-Fock-Theory-for-Molecules)
+## [Hartree-Fock (HF) Theory](Hartree-Fock-Theory-for-Molecules.md)
 
 <!-- end list -->
 
-## [Density Functional Theory (DFT)](Density-Functional-Theory-for-Molecules)
+## [Density Functional Theory (DFT)](Density-Functional-Theory-for-Molecules.md)
 
 <!-- end list -->
 
-## [Excited-State Calculations (CIS, TDHF, TDDFT)](Excited-State-Calculations)
+## [Excited-State Calculations (CIS, TDHF, TDDFT)](Excited-State-Calculations.md)
 
 <!-- end list -->
 
-## [Real-time TDDFT](RT-TDDFT)
+## [Real-time TDDFT](RT-TDDFT.md)
 
 <!-- end list -->
 
-## [Plane-Wave Density Functional Theory (plane-wave DFT)](Plane-Wave-Density-Functional-Theory)
+## [Plane-Wave Density Functional Theory (plane-wave DFT)](Plane-Wave-Density-Functional-Theory.md)
 
 <!-- end list -->
 
-## [Tensor Contraction Engine: CI, MBPT, and CC](TCE)
+## [Tensor Contraction Engine: CI, MBPT, and CC](TCE.md)
 
 <!-- end list -->
 
-## [MP2](MP2)
+## [MP2](MP2.md)
 
 <!-- end list -->
 
-## [Coupled Cluster Calculations](CCSD)
+## [Coupled Cluster Calculations](CCSD.md)
 
 <!-- end list -->
 
-## [Multiconfiguration SCF](Multiconfiguration_SCF)
+## [Multiconfiguration SCF](Multiconfiguration_SCF.md)
 
 <!-- end list -->
 
-## [GW calculations](GW)
+## [GW calculations](GW.md)
 
 <!-- end list -->
 
diff --git a/Quantum-Molecular-Dynamics.md b/Quantum-Molecular-Dynamics.md
index d5051535..d3e859f5 100644
--- a/Quantum-Molecular-Dynamics.md
+++ b/Quantum-Molecular-Dynamics.md
@@ -1,6 +1,6 @@
 # Quantum Molecular Dynamics
 
-## [Plane-Wave Basis](Plane-Wave-Density-Functional-Theory)
+## [Plane-Wave Basis](Plane-Wave-Density-Functional-Theory.md)
 
 
-## [Gaussian Basis AIMD](Gaussian-Basis-AIMD)
+## [Gaussian Basis AIMD](Gaussian-Basis-AIMD.md)
diff --git a/Supplementary-Information.md b/Supplementary-Information.md
index ca296781..f93d84c6 100644
--- a/Supplementary-Information.md
+++ b/Supplementary-Information.md
@@ -1,5 +1,7 @@
-  - [Global Arrays](http://hpc.pnl.gov/globalarrays/)
+# Supplementary Information
 
-  - [Choosing the right ARMCI library](ARMCI)
+## [Global Arrays](http://hpc.pnl.gov/globalarrays/)
 
-  - [Software supporting NWChem](Software-supporting-NWChem)
+## [Choosing the right ARMCI library](ARMCI.md)
+
+## [Software supporting NWChem](Software-supporting-NWChem.md)