diff --git a/base/data/src/main/java/org/openscience/cdk/Element.java b/base/data/src/main/java/org/openscience/cdk/Element.java
index b6eaabc313..f06a248637 100644
--- a/base/data/src/main/java/org/openscience/cdk/Element.java
+++ b/base/data/src/main/java/org/openscience/cdk/Element.java
@@ -115,12 +115,12 @@ public Element(String symbol, Integer atomicNumber) {
      *  <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Elements can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Element element = new Element("C");
      *   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
      *   if.configure(element);
      * </pre>
-     * </p>
      *
      * @return The atomic number of this element
      *
diff --git a/base/data/src/main/java/org/openscience/cdk/Isotope.java b/base/data/src/main/java/org/openscience/cdk/Isotope.java
index 3877e38e0b..8bcd53992a 100644
--- a/base/data/src/main/java/org/openscience/cdk/Isotope.java
+++ b/base/data/src/main/java/org/openscience/cdk/Isotope.java
@@ -178,12 +178,12 @@ public void setExactMass(Double exactMass) {
      *  <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return    The NaturalAbundance value
      *
@@ -199,12 +199,12 @@ public Double getNaturalAbundance() {
      *  <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return    The ExactMass value
      *
@@ -221,12 +221,12 @@ public Double getExactMass() {
      * <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return The atomic mass of this element
      *
diff --git a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java
index 9fa75438f5..a90e47ee3d 100644
--- a/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java
+++ b/base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java
@@ -40,7 +40,6 @@ public interface IElement extends IChemObject {
      *   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
      *   if.configure(element);
      * </pre>
-     * </p>
      *
      * @return The atomic number of this element
      *
diff --git a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
index 1fddbc9ef0..71a702cea5 100644
--- a/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
+++ b/base/isomorphism/src/main/java/org/openscience/cdk/isomorphism/matchers/QueryAtom.java
@@ -487,12 +487,12 @@ public void setExactMass(Double exactMass) {
      *  <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return    The NaturalAbundance value
      *
@@ -508,12 +508,12 @@ public Double getNaturalAbundance() {
      *  <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return    The ExactMass value
      *
@@ -530,12 +530,12 @@ public Double getExactMass() {
      * <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Isotopes can be configured by using
      * the IsotopeFactory.configure() method:
+     * </p>
      * <pre>
      *   Isotope isotope = new Isotope("C", 13);
      *   IsotopeFactory if = IsotopeFactory.getInstance(isotope.getNewBuilder());
      *   if.configure(isotope);
      * </pre>
-     * </p>
      *
      * @return The atomic mass of this element
      *
@@ -562,15 +562,14 @@ public void setMassNumber(Integer massNumber) {
     /**
      * Returns the atomic number of this element.
      *
-     *  <p>Once instantiated all field not filled by passing parameters
+     * <p>Once instantiated all field not filled by passing parameters
      * to the constructor are null. Elements can be configured by using
-     * the IsotopeFactory.configure() method:
+     * the IsotopeFactory.configure() method:</p>
      * <pre>
      *   Element element = new Element("C");
      *   IsotopeFactory if = IsotopeFactory.getInstance(element.getNewBuilder());
      *   if.configure(element);
      * </pre>
-     * </p>
      *
      * @return The atomic number of this element
      *
diff --git a/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java b/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
index fde885a0e2..87f222a9d2 100644
--- a/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
+++ b/base/standard/src/main/java/org/openscience/cdk/fingerprint/HybridizationFingerprinter.java
@@ -50,14 +50,14 @@
  * exclude candidates for a substructure search in a database. They are also a
  * means for determining the similarity of chemical structures.
  *
- * <p>A fingerprint is generated for an AtomContainer with this code:<pre>
+ * <p>A fingerprint is generated for an AtomContainer with this code:</p><pre>
  *   Molecule molecule = new Molecule();
  *   IFingerprinter fingerprinter =
  *     new HybridizationFingerprinter();
  *   BitSet fingerprint = fingerprinter.getFingerprint(molecule);
  *   fingerprint.size(); // returns 1024 by default
  *   fingerprint.length(); // returns the highest set bit
- * </pre></p>
+ * </pre>
  *
  * <p>The FingerPrinter assumes that hydrogens are explicitly given!
  * Furthermore, if pseudo atoms or atoms with malformed symbols are present,
diff --git a/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java b/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
index 985b050955..456d41550b 100755
--- a/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
+++ b/base/standard/src/main/java/org/openscience/cdk/graph/AtomContainerAtomPermutor.java
@@ -28,9 +28,9 @@
 
 /**
  * An atom container atom permutor that uses ranking and unranking to calculate
- * the next permutation in the series.</p>
+ * the next permutation in the series.
  *
- * <p>Typical use:<pre>
+ * <p>Typical use:</p><pre>
  * AtomContainerAtomPermutor permutor = new AtomContainerAtomPermutor(container);
  * while (permutor.hasNext()) {
  *   IAtomContainer permutedContainer = permutor.next();