diff --git a/avogadro/qtplugins/spectra/spectra.cpp b/avogadro/qtplugins/spectra/spectra.cpp
index 39b424334c..4389dd2ea1 100644
--- a/avogadro/qtplugins/spectra/spectra.cpp
+++ b/avogadro/qtplugins/spectra/spectra.cpp
@@ -106,6 +106,10 @@ void Spectra::openDialog()
   }
 
   gatherSpectra();
+  // update the elements
+  auto elements = m_molecule->atomicNumbers();
+  std::vector<unsigned char> atomicNumbers(elements.begin(), elements.end());
+  m_dialog->setElements(atomicNumbers);
   m_dialog->show();
 }
 
diff --git a/avogadro/qtplugins/spectra/spectradialog.cpp b/avogadro/qtplugins/spectra/spectradialog.cpp
index 730c4484dc..0576273907 100644
--- a/avogadro/qtplugins/spectra/spectradialog.cpp
+++ b/avogadro/qtplugins/spectra/spectradialog.cpp
@@ -37,12 +37,26 @@ float scaleAndBlur(float x, float peak, float intensity, float scale = 1.0,
 
   // x is the absolute position, but we need to scale the peak position
   float scaled_peak = (peak - shift) / scale;
+
   float delta = x - scaled_peak;
   float exponent = -(delta * delta) / (2 * sigma * sigma);
   float gaussian = exp(exponent);
   return intensity * gaussian;
 }
 
+float closestTo(float x, float peak, float intensity, float scale = 1.0,
+                float shift = 0.0, float xScale = 1.0)
+{
+  // return peak intensity if x is closer to the peak than another point
+  // scaled by scale and shifted by shift
+  float scaled_peak = (peak - shift) / scale;
+  float delta = x - scaled_peak;
+  // xScale is the reciprocal of the space between points
+  // (i.e., used to generate many points in the loop)
+  float peak_to_peak = 1.0 / xScale;
+  return (fabs(delta) < peak_to_peak / 2.0) ? intensity : 0.0;
+}
+
 std::vector<double> fromMatrix(const MatrixX& matrix)
 {
   std::vector<double> result;
@@ -55,6 +69,14 @@ SpectraDialog::SpectraDialog(QWidget* parent)
   : QDialog(parent), m_ui(new Ui::SpectraDialog)
 {
   m_ui->setupUi(this);
+
+  // hide the units for now
+  m_ui->unitsLabel->hide();
+  m_ui->unitsCombo->hide();
+
+  // only for NMR
+  m_ui->elementCombo->hide();
+
   m_ui->dataTable->horizontalHeader()->setSectionResizeMode(
     QHeaderView::Stretch);
 
@@ -63,6 +85,8 @@ SpectraDialog::SpectraDialog(QWidget* parent)
   m_ui->dataTable->hide();
   m_ui->push_exportData->hide();
 
+  readSettings();
+
   // connections for options
   connect(m_ui->push_options, SIGNAL(clicked()), this, SLOT(toggleOptions()));
   connect(m_ui->push_colorBackground, SIGNAL(clicked()), this,
@@ -77,6 +101,17 @@ SpectraDialog::SpectraDialog(QWidget* parent)
           SLOT(changeFontSize()));
   connect(m_ui->lineWidthSpinBox, SIGNAL(valueChanged(double)), this,
           SLOT(changeLineWidth()));
+  connectOptions();
+}
+
+SpectraDialog::~SpectraDialog()
+{
+  writeSettings();
+}
+
+void SpectraDialog::connectOptions()
+{
+  // connect (or reconnect) anything that calls change or update plot
   connect(m_ui->combo_spectra, SIGNAL(currentIndexChanged(int)), this,
           SLOT(changeSpectra()));
   connect(m_ui->xAxisMinimum, SIGNAL(valueChanged(double)), this,
@@ -89,103 +124,300 @@ SpectraDialog::SpectraDialog(QWidget* parent)
           SLOT(updatePlot()));
   connect(m_ui->peakWidth, SIGNAL(valueChanged(double)), this,
           SLOT(updatePlot()));
+}
 
-  readSettings();
+void SpectraDialog::disconnectOptions()
+{
+  // disconnect anything that calls change or update plot
+  disconnect(m_ui->combo_spectra, SIGNAL(currentIndexChanged(int)), this,
+             SLOT(changeSpectra()));
+  disconnect(m_ui->xAxisMinimum, SIGNAL(valueChanged(double)), this,
+             SLOT(updatePlot()));
+  disconnect(m_ui->xAxisMaximum, SIGNAL(valueChanged(double)), this,
+             SLOT(updatePlot()));
+  disconnect(m_ui->yAxisMinimum, SIGNAL(valueChanged(double)), this,
+             SLOT(updatePlot()));
+  disconnect(m_ui->yAxisMaximum, SIGNAL(valueChanged(double)), this,
+             SLOT(updatePlot()));
+  disconnect(m_ui->peakWidth, SIGNAL(valueChanged(double)), this,
+             SLOT(updatePlot()));
 }
 
-SpectraDialog::~SpectraDialog()
+void SpectraDialog::updateElementCombo()
 {
-  writeSettings();
+  // update the element combo box
+  disconnect(m_ui->elementCombo, SIGNAL(currentIndexChanged(int)), this,
+             SLOT(changeSpectra()));
+  m_ui->elementCombo->clear();
+
+  // go through the elements in atomic number order
+  // make a copy of the vector
+  std::vector<unsigned char> elements = m_elements;
+  std::sort(elements.begin(), elements.end());
+
+  // add the unique elements, with the element number as the data
+  for (auto& element : elements) {
+    // check to see if it's already in the combo box
+    bool found = false;
+    for (int i = 0; i < m_ui->elementCombo->count(); ++i) {
+      if (m_ui->elementCombo->itemData(i).toInt() == element) {
+        found = true;
+        break;
+      }
+    }
+    if (found)
+      continue;
+
+    switch (element) {
+      case 1:
+        m_ui->elementCombo->addItem("¹H", element);
+        break;
+      case 3:
+        m_ui->elementCombo->addItem("⁷Li", element);
+        break;
+      case 5:
+        m_ui->elementCombo->addItem("¹¹B", element);
+        break;
+      case 6:
+        m_ui->elementCombo->addItem("¹³C", element);
+        break;
+      case 7:
+        m_ui->elementCombo->addItem("¹⁵N", element);
+        break;
+      case 8:
+        m_ui->elementCombo->addItem("¹⁷O", element);
+        break;
+      case 9:
+        m_ui->elementCombo->addItem("¹⁹F", element);
+        break;
+      case 14:
+        m_ui->elementCombo->addItem("²⁹Si", element);
+        break;
+      case 15:
+        m_ui->elementCombo->addItem("³¹P", element);
+        break;
+      default:
+        m_ui->elementCombo->addItem(QString::number(element), element);
+        break;
+    }
+  }
+
+  // connect the element combo box
+  connect(m_ui->elementCombo, SIGNAL(currentIndexChanged(int)), this,
+          SLOT(changeSpectra()));
+  changeSpectra(); // default to 1H
 }
 
 void SpectraDialog::changeSpectra()
 {
-  // TODO: change the scale and offset based on defaults and settings
+  // based on the current spectra type, update the options
+  // and prep the spectra for plotting
   QSettings settings;
 
+  disconnectOptions();
+
   // what type of spectra are we plotting?
   SpectraType type =
     static_cast<SpectraType>(m_ui->combo_spectra->currentData().toInt());
 
+  // only show for NMR
+  m_ui->elementCombo->hide();
+  // todo: some spectra might want to swtich units
+
+  m_transitions.clear();
+  m_intensities.clear();
+
   switch (type) {
     case SpectraType::Infrared:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
-      m_ui->xAxisMinimum->setValue(4000.0);
-      m_ui->xAxisMaximum->setValue(0.0);
-      m_ui->peakWidth->setValue(30.0);
+      m_transitions = fromMatrix(m_spectra["IR"].col(0));
+      m_intensities = fromMatrix(m_spectra["IR"].col(1));
+
+      settings.beginGroup("spectra/ir");
+      m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+      m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+      m_ui->xAxisMinimum->setValue(settings.value("xmin", 4000.0).toDouble());
+      m_ui->xAxisMaximum->setValue(settings.value("xmax", 400.0).toDouble());
+      m_ui->peakWidth->setValue(settings.value("fwhm", 30.0).toDouble());
+      settings.endGroup();
       break;
     case SpectraType::Raman:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
-      m_ui->xAxisMinimum->setValue(0.0);
-      m_ui->xAxisMaximum->setValue(4000.0);
-      m_ui->peakWidth->setValue(30.0);
+      m_transitions = fromMatrix(m_spectra["Raman"].col(0));
+      m_intensities = fromMatrix(m_spectra["Raman"].col(1));
+
+      settings.beginGroup("spectra/raman");
+      m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+      m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+      m_ui->xAxisMinimum->setValue(settings.value("xmin", 0.0).toDouble());
+      m_ui->xAxisMaximum->setValue(settings.value("xmax", 4000.0).toDouble());
+      m_ui->peakWidth->setValue(settings.value("fwhm", 30.0).toDouble());
+      settings.endGroup();
       break;
     case SpectraType::NMR:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
-      // todo: these should be per element
-      m_ui->xAxisMinimum->setValue(0.0);
-      m_ui->xAxisMaximum->setValue(200.0);
-      m_ui->peakWidth->setValue(0.1);
+      // settings handled per-element below
+      m_ui->elementCombo->show();
       break;
     case SpectraType::Electronic:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
+      m_transitions = fromMatrix(m_spectra["Electronic"].col(0));
+      m_intensities = fromMatrix(m_spectra["Electronic"].col(1));
+
+      settings.beginGroup("spectra/electronic");
+      m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+      m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
       // in eV
-      m_ui->xAxisMinimum->setValue(5.0);
-      m_ui->xAxisMaximum->setValue(1.0);
-      m_ui->peakWidth->setValue(0.1);
+      m_ui->xAxisMinimum->setValue(settings.value("xmin", 5.0).toDouble());
+      m_ui->xAxisMaximum->setValue(settings.value("xmax", 1.0).toDouble());
+      m_ui->peakWidth->setValue(settings.value("fwhm", 0.1).toDouble());
+      settings.endGroup();
       break;
     case SpectraType::CircularDichroism:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
-      m_ui->xAxisMinimum->setValue(5.0);
-      m_ui->xAxisMaximum->setValue(1.0);
-      m_ui->peakWidth->setValue(0.1);
+      m_transitions = fromMatrix(m_spectra["Electronic"].col(0));
+      // check if electronic has a third column
+      if (m_spectra["Electronic"].cols() > 2)
+        m_intensities = fromMatrix(m_spectra["Electronic"].col(2));
+      else // grab it from the CD data
+        m_intensities = fromMatrix(m_spectra["CircularDichroism"].col(1));
+
+      settings.beginGroup("spectra/cd");
+      m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+      m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+      // default to eV units
+      m_ui->xAxisMinimum->setValue(settings.value("xmin", 5.0).toDouble());
+      m_ui->xAxisMaximum->setValue(settings.value("xmax", 1.0).toDouble());
+      m_ui->peakWidth->setValue(settings.value("fwhm", 0.1).toDouble());
+      settings.endGroup();
       break;
     case SpectraType::DensityOfStates:
-      m_ui->scaleSpinBox->setValue(1.0);
-      m_ui->offsetSpinBox->setValue(0.0);
-      m_ui->xAxisMinimum->setValue(-50.0);
-      m_ui->xAxisMaximum->setValue(50.0);
-      m_ui->peakWidth->setValue(0.1);
+      m_transitions = fromMatrix(m_spectra["DensityOfStates"].col(0));
+      m_intensities = fromMatrix(m_spectra["DensityOfStates"].col(1));
+
+      settings.beginGroup("spectra/dos");
+      m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+      m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+      m_ui->xAxisMinimum->setValue(settings.value("xmin", -50.0).toDouble());
+      m_ui->xAxisMaximum->setValue(settings.value("xmax", 50.0).toDouble());
+      m_ui->peakWidth->setValue(settings.value("fwhm", 0.1).toDouble());
+      settings.endGroup();
       break;
   }
 
-  MatrixX& spectra =
-    m_spectra[m_ui->combo_spectra->currentText().toStdString()];
-  float maxIntensity = 1.0;
-  // update the data table
-  m_ui->dataTable->setRowCount(spectra.rows());
-  m_ui->dataTable->setColumnCount(spectra.cols());
-  for (auto i = 0; i < spectra.rows(); ++i) {
-    for (auto j = 0; j < spectra.cols(); ++j) {
-      QTableWidgetItem* item =
-        new QTableWidgetItem(QString::number(spectra(i, j), 'f', 4));
-      m_ui->dataTable->setItem(i, j, item);
+  // a bunch of special work depending on the NMR element
+  if (type == SpectraType::NMR) {
+    // get the element
+    int element = m_ui->elementCombo->currentData().toInt();
+
+    settings.beginGroup(QString("spectra/nmr/%1").arg(element));
+    m_ui->scaleSpinBox->setValue(settings.value("scale", 1.0).toDouble());
+    m_ui->peakWidth->setValue(settings.value("fwhm", 0.1).toDouble());
+
+    // tweak the default axis range
+    // based on https://imserc.northwestern.edu/guide/eNMR/chem/NMRnuclei.html
+    // offsets are approximate from a few calculations
+    // .. to at least provide a starting point
+    switch (element) {
+      case 1: // 1H
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 12.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", 0.0).toDouble());
+        m_ui->offsetSpinBox->setValue(
+          settings.value("offset", 31.876).toDouble());
+        break;
+      case 3: // 7Li
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", -16.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", 11.0).toDouble());
+        // TODO: offset
+        m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+        break;
+      case 5: // 11B
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 100.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -120.0).toDouble());
+        // TODO: offset
+        m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+        break;
+      case 6: // 13C
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 200.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", 0.0).toDouble());
+        m_ui->offsetSpinBox->setValue(
+          settings.value("offset", 192.038).toDouble());
+        break;
+      case 7: // 15N
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 800.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", 0.0).toDouble());
+        m_ui->offsetSpinBox->setValue(
+          settings.value("offset", -106.738).toDouble());
+        break;
+      case 8: // 17O
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 1600.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -50.0).toDouble());
+        // TODO: offset
+        m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+        break;
+      case 9: // 19F
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 60.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -300.0).toDouble());
+        m_ui->offsetSpinBox->setValue(
+          settings.value("offset", 206.735).toDouble());
+        break;
+      case 14: // 29Si
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 50.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -200.0).toDouble());
+        m_ui->offsetSpinBox->setValue(
+          settings.value("offset", 400.876).toDouble());
+        break;
+      case 15: // 31P
+        m_ui->xAxisMinimum->setValue(settings.value("xmin", 250.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -250.0).toDouble());
+        // TODO: offset
+        m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+        break;
+      default:
+        m_ui->xAxisMinimum->setValue(settings.value("xmax", 100.0).toDouble());
+        m_ui->xAxisMaximum->setValue(settings.value("xmax", -100.0).toDouble());
+        m_ui->offsetSpinBox->setValue(settings.value("offset", 0.0).toDouble());
+        break;
     }
-  }
-  // if there's a second column, check for intensities
-  if (spectra.cols() > 1) {
-    for (auto i = 0; i < spectra.rows(); ++i) {
-      if (spectra(i, 1) > maxIntensity)
-        maxIntensity = spectra(i, 1);
+    settings.endGroup();
+
+    // the default NMR data has all the atoms in it,
+    // so we need to loop through m_elements to filter
+    MatrixX nmr = m_spectra["NMR"];
+
+    for (int i = 0; i < m_elements.size(); ++i) {
+      if (m_elements[i] == element) {
+        m_transitions.push_back(nmr(i, 0));
+      }
     }
-    maxIntensity = maxIntensity * 1.25;
+    // fill the intensities with 1.0
+    m_intensities.resize(m_transitions.size(), 1.0);
   }
-  // if transmission for IR, set the max intensity to 100
-  if (type == SpectraType::Infrared)
-    maxIntensity = 100.0;
+  // other spectra transitions and intensities are already set
 
-  if (maxIntensity < 1.0)
-    maxIntensity = 1.0;
+  // update the data table
+  double maxIntensity = 0.0;
+  m_ui->dataTable->setRowCount(m_transitions.size());
+  m_ui->dataTable->setColumnCount(2);
+  for (auto i = 0; i < m_transitions.size(); ++i) {
+    // frequency or energy
+    QTableWidgetItem* item =
+      new QTableWidgetItem(QString::number(m_transitions[i], 'f', 4));
+    m_ui->dataTable->setItem(i, 0, item);
+    // intensities
+    item = new QTableWidgetItem(QString::number(m_intensities[i], 'f', 4));
+    m_ui->dataTable->setItem(i, 1, item);
+
+    if (m_intensities[i] > maxIntensity)
+      maxIntensity = m_intensities[i];
+  }
 
-  // update the spin box
+  // update the spin boxes
   m_ui->yAxisMaximum->setValue(maxIntensity);
+  m_ui->yAxisMinimum->setMinimum(0.0);
+  // if CD, set the minimum too
+  if (type == SpectraType::CircularDichroism) {
+    m_ui->yAxisMinimum->setMinimum(-maxIntensity * 2.0);
+    m_ui->yAxisMinimum->setValue(-maxIntensity);
+  }
 
   updatePlot();
+  connectOptions();
 }
 
 void SpectraDialog::setSpectra(const std::map<std::string, MatrixX>& spectra)
@@ -193,9 +425,13 @@ void SpectraDialog::setSpectra(const std::map<std::string, MatrixX>& spectra)
   m_spectra = spectra;
 
   // update the combo box
+  disconnect(m_ui->combo_spectra, SIGNAL(currentIndexChanged(int)), this,
+             SLOT(changeSpectra()));
+
   m_ui->combo_spectra->clear();
   for (auto& spectra : m_spectra) {
     QString name = QString::fromStdString(spectra.first);
+
     if (name == "IR") {
       name = tr("Infrared");
       m_ui->combo_spectra->addItem(name,
@@ -222,7 +458,9 @@ void SpectraDialog::setSpectra(const std::map<std::string, MatrixX>& spectra)
   }
 
   changeSpectra();
-  updatePlot();
+  // connect again
+  connect(m_ui->combo_spectra, SIGNAL(currentIndexChanged(int)), this,
+          SLOT(changeSpectra()));
 }
 
 void SpectraDialog::writeSettings() const
@@ -236,21 +474,24 @@ void SpectraDialog::writeSettings() const
 void SpectraDialog::readSettings()
 {
   QSettings settings;
+  settings.beginGroup("spectra");
   // update the dialog with saved settings
 
   // font size
-  int fontSize = settings.value("spectra/fontSize", 12).toInt();
+  int fontSize = settings.value("fontSize", 12).toInt();
   m_ui->fontSizeCombo->setCurrentText(QString::number(fontSize));
   // line width
-  float lineWidth = settings.value("spectra/lineWidth", 1.0).toFloat();
+  float lineWidth = settings.value("lineWidth", 1.0).toFloat();
   m_ui->lineWidthSpinBox->setValue(lineWidth);
+
+  // TODO: other bits
+  settings.endGroup();
 }
 
 void SpectraDialog::changeBackgroundColor()
 {
   QSettings settings;
-  QColor current =
-    settings.value("spectra/backgroundColor", white).value<QColor>();
+  QColor current = settings.value("backgroundColor", white).value<QColor>();
   QColor color =
     QColorDialog::getColor(current, this, tr("Select Background Color"));
   if (color.isValid() && color != current) {
@@ -319,6 +560,9 @@ void SpectraDialog::changeLineWidth()
 
 void SpectraDialog::updatePlot()
 {
+  // disconnect the options while we update the plot
+  disconnectOptions();
+
   // the raw data
   std::vector<double> transitions, intensities;
   // for the plot
@@ -332,123 +576,144 @@ void SpectraDialog::updatePlot()
   QString windowName;
   QString xTitle;
   QString yTitle;
+  // TODO: switch units for electronic and CD
+  QString xWave = tr("Wavelength (nm)");
+
   bool transmission = false;
   // get the raw data from the spectra map
   switch (type) {
     case SpectraType::Infrared:
-      transitions = fromMatrix(m_spectra["IR"].col(0));
-      intensities = fromMatrix(m_spectra["IR"].col(1));
       windowName = tr("Vibrational Spectra");
       xTitle = tr("Wavenumbers (cm⁻¹)");
       yTitle = tr("Transmission");
       transmission = true;
 
-      settings.setValue("spectra/irXMin", float(m_ui->xAxisMinimum->value()));
-      settings.setValue("spectra/irXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/irPeakWidth", float(m_ui->peakWidth->value()));
-      settings.setValue("spectra/irScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/irOffset", m_ui->offsetSpinBox->value());
+      settings.beginGroup("spectra/ir");
+      settings.setValue("xmin", float(m_ui->xAxisMinimum->value()));
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", float(m_ui->peakWidth->value()));
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
     case SpectraType::Raman:
-      transitions = fromMatrix(m_spectra["Raman"].col(0));
-      intensities = fromMatrix(m_spectra["Raman"].col(1));
       windowName = tr("Raman Spectra");
       xTitle = tr("Wavenumbers (cm⁻¹)");
       yTitle = tr("Intensity");
       // save the plot settings
-      settings.setValue("spectra/ramanXMin", m_ui->xAxisMinimum->value());
-      settings.setValue("spectra/ramanXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/ramanPeakWidth", m_ui->peakWidth->value());
-      settings.setValue("spectra/ramanScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/ramanOffset", m_ui->offsetSpinBox->value());
+      settings.beginGroup("spectra/raman");
+      settings.setValue("xmin", m_ui->xAxisMinimum->value());
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", m_ui->peakWidth->value());
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
     case SpectraType::NMR:
-      transitions = fromMatrix(m_spectra["NMR"].col(0));
-      intensities = fromMatrix(m_spectra["NMR"].col(1));
       windowName = tr("NMR Spectra");
       xTitle = tr("Chemical Shift (ppm)");
       yTitle = tr("Intensity");
-      // save the plot settings
-      settings.setValue("spectra/nmrXMin", m_ui->xAxisMinimum->value());
-      settings.setValue("spectra/nmrXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/nmrPeakWidth", m_ui->peakWidth->value());
-      settings.setValue("spectra/nmrScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/nmrOffset", m_ui->offsetSpinBox->value());
+      // save the plot settings on a per element basis
+      settings.beginGroup(QString("spectra/nmr/%1")
+                            .arg(m_ui->elementCombo->currentData().toInt()));
+      settings.setValue("xmin", m_ui->xAxisMinimum->value());
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", m_ui->peakWidth->value());
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
     case SpectraType::Electronic:
-      transitions = fromMatrix(m_spectra["Electronic"].col(0));
-      intensities = fromMatrix(m_spectra["Electronic"].col(1));
       windowName = tr("Electronic Spectra");
-      xTitle = tr("eV");
+      xTitle = tr("Energy (eV)");
       yTitle = tr("Intensity");
       // save settings
-      settings.setValue("spectra/electronicXMin", m_ui->xAxisMinimum->value());
-      settings.setValue("spectra/electronicXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/electronicPeakWidth",
-                        m_ui->peakWidth->value());
-      settings.setValue("spectra/electronicScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/electronicOffset",
-                        m_ui->offsetSpinBox->value());
+      settings.beginGroup("spectra/electronic");
+      settings.setValue("xmin", m_ui->xAxisMinimum->value());
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", m_ui->peakWidth->value());
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
     case SpectraType::CircularDichroism:
-      transitions = fromMatrix(m_spectra["Electronic"].col(0));
-      intensities = fromMatrix(m_spectra["Electronic"].col(2));
       windowName = tr("Circular Dichroism Spectra");
-      xTitle = tr("eV)");
+      xTitle = tr("Energy (eV)");
       yTitle = tr("Intensity");
       // save settings
-      settings.setValue("spectra/CDXMin", m_ui->xAxisMinimum->value());
-      settings.setValue("spectra/CDXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/CDPeakWidth", m_ui->peakWidth->value());
-      settings.setValue("spectra/CDScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/CDOffset", m_ui->offsetSpinBox->value());
+      settings.beginGroup("spectra/cd");
+      settings.setValue("xmin", m_ui->xAxisMinimum->value());
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", m_ui->peakWidth->value());
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
     case SpectraType::DensityOfStates:
-      transitions = fromMatrix(m_spectra["DensityOfStates"].col(0));
-      intensities = fromMatrix(m_spectra["DensityOfStates"].col(1));
       windowName = tr("Density of States");
-      xTitle = tr("eV");
-      yTitle = tr("Intensity");
+      xTitle = tr("Energy (eV)");
+      yTitle = tr("Density");
       // save settings
-      settings.setValue("spectra/dosXMin", m_ui->xAxisMinimum->value());
-      settings.setValue("spectra/dosXMax", m_ui->xAxisMaximum->value());
-      settings.setValue("spectra/dosPeakWidth", m_ui->peakWidth->value());
-      settings.setValue("spectra/dosScale", m_ui->scaleSpinBox->value());
-      settings.setValue("spectra/dosOffset", m_ui->offsetSpinBox->value());
+      settings.beginGroup("spectra/dos");
+      settings.setValue("xmin", m_ui->xAxisMinimum->value());
+      settings.setValue("xmax", m_ui->xAxisMaximum->value());
+      settings.setValue("fwhm", m_ui->peakWidth->value());
+      settings.setValue("scale", m_ui->scaleSpinBox->value());
+      settings.setValue("offset", m_ui->offsetSpinBox->value());
+      settings.endGroup();
       break;
   }
   setWindowTitle(windowName);
 
   double maxIntensity = 0.0f;
-  for (auto intensity : intensities) {
+  for (auto intensity : m_intensities) {
     if (intensity > maxIntensity)
       maxIntensity = intensity;
   }
 
+  // if transmission for IR, set the max intensity to 100
+  if (type == SpectraType::Infrared)
+    maxIntensity = 100.0;
+
+  if (maxIntensity < 1.0)
+    maxIntensity = 1.0;
+
   // now compose the plot data
   float scale = m_ui->scaleSpinBox->value();
   float offset = m_ui->offsetSpinBox->value();
+  // NMR offsets should be inverted
+  if (type == SpectraType::NMR) {
+    scale = -scale;
+  }
+
   float fwhm = m_ui->peakWidth->value();
 
   float xMin = m_ui->xAxisMinimum->value();
   float xMax = m_ui->xAxisMaximum->value();
 
-  int start = std::min(static_cast<int>(xMin), static_cast<int>(xMax));
-  int end = std::max(static_cast<int>(xMin), static_cast<int>(xMax));
-
-  for (unsigned int x = start; x < end; ++x) {
-    float xValue = static_cast<float>(x);
+  float start = std::min(xMin, xMax);
+  float end = std::max(xMin, xMax);
+  // for some spectra, we need to take small steps, so we scale the x axis
+  float xScale = 1.0;
+  if (type == SpectraType::Electronic || type == SpectraType::CircularDichroism)
+    xScale = 1.0f / 0.05f;
+  else if (type == SpectraType::NMR)
+    xScale = 1.0f / 0.01f;
+
+  // TODO: process an experimental spectrum via interpolation
+  for (unsigned int x = round(start * xScale); x < round(end * xScale); ++x) {
+    float xValue = static_cast<float>(x) / xScale;
     xData.push_back(xValue);
     yData.push_back(0.0f);
     yStick.push_back(0.0f);
 
     // now we add up the intensity from any frequency
-    for (auto index = 0; index < transitions.size(); ++index) {
-      float freq = transitions[index];
-      float peak = intensities[index];
+    for (auto index = 0; index < m_transitions.size(); ++index) {
+      float freq = m_transitions[index];
+      float peak = m_intensities[index];
 
       float intensity = scaleAndBlur(xValue, freq, peak, scale, offset, fwhm);
-      float stick = scaleAndBlur(xValue, freq, peak, scale, offset, 1.0);
+      float stick = closestTo(xValue, freq, peak, scale, offset, xScale);
 
       yData.back() += intensity;
       yStick.back() += stick;
@@ -492,6 +757,9 @@ void SpectraDialog::updatePlot()
 
   chart->setXAxisLimits(xAxisMin, xAxisMax);
   chart->setYAxisLimits(yAxisMin, yAxisMax);
+
+  // re-enable the options
+  connectOptions();
 }
 
 VTK::ChartWidget* SpectraDialog::chartWidget()
diff --git a/avogadro/qtplugins/spectra/spectradialog.h b/avogadro/qtplugins/spectra/spectradialog.h
index 4b96a74a4a..0e22496b5c 100644
--- a/avogadro/qtplugins/spectra/spectradialog.h
+++ b/avogadro/qtplugins/spectra/spectradialog.h
@@ -45,9 +45,17 @@ class SpectraDialog : public QDialog
   void readSettings();
 
   void setSpectra(const std::map<std::string, MatrixX>& spectra);
+  void setElements(const std::vector<unsigned char>& elements)
+  {
+    m_elements = elements;
+    updateElementCombo();
+  }
 
   VTK::ChartWidget* chartWidget();
 
+  void disconnectOptions();
+  void connectOptions();
+
 private slots:
   void changeBackgroundColor();
   void changeForegroundColor();
@@ -57,14 +65,19 @@ private slots:
   void changeLineWidth();
   void changeSpectra();
 
+  void updateElementCombo();
   void updatePlot();
 
   void toggleOptions();
 
 private:
   std::map<std::string, MatrixX> m_spectra;
+  std::vector<unsigned char> m_elements; // for NMR
+  // current spectra data
+  std::vector<double> m_transitions;
+  std::vector<double> m_intensities;
 
-  QString m_currentSpectra;
+  QString m_currentSpectraType;
   Ui::SpectraDialog* m_ui;
 };
 
diff --git a/avogadro/qtplugins/spectra/spectradialog.ui b/avogadro/qtplugins/spectra/spectradialog.ui
index 2d0574af20..9ca79bd1a3 100644
--- a/avogadro/qtplugins/spectra/spectradialog.ui
+++ b/avogadro/qtplugins/spectra/spectradialog.ui
@@ -23,43 +23,7 @@
    <bool>true</bool>
   </property>
   <layout class="QGridLayout" name="gridLayout">
-   <item row="5" column="1">
-    <widget class="QPushButton" name="push_loadSpectra">
-     <property name="enabled">
-      <bool>false</bool>
-     </property>
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-     <property name="text">
-      <string>&amp;Load data...</string>
-     </property>
-    </widget>
-   </item>
-   <item row="9" column="7">
-    <widget class="QPushButton" name="push_exportData">
-     <property name="text">
-      <string>Export Data</string>
-     </property>
-    </widget>
-   </item>
-   <item row="5" column="3">
-    <widget class="QPushButton" name="pushButton">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-     <property name="text">
-      <string>&amp;Close</string>
-     </property>
-    </widget>
-   </item>
-   <item row="8" column="0" rowspan="2" colspan="4">
+   <item row="8" column="0" rowspan="2" colspan="5">
     <widget class="QTabWidget" name="tab_widget">
      <property name="sizePolicy">
       <sizepolicy hsizetype="Expanding" vsizetype="Fixed">
@@ -80,6 +44,9 @@
          <property name="alignment">
           <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
          </property>
+         <property name="minimum">
+          <double>-4000.000000000000000</double>
+         </property>
          <property name="maximum">
           <double>4000.000000000000000</double>
          </property>
@@ -196,7 +163,7 @@
           <set>Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter</set>
          </property>
          <property name="minimum">
-          <double>1.000000000000000</double>
+          <double>0.010000000000000</double>
          </property>
         </widget>
        </item>
@@ -217,6 +184,20 @@
          </property>
         </widget>
        </item>
+       <item row="0" column="0">
+        <widget class="QLabel" name="unitsLabel">
+         <property name="text">
+          <string>Units:</string>
+         </property>
+        </widget>
+       </item>
+       <item row="0" column="1">
+        <widget class="QComboBox" name="unitsCombo">
+         <property name="enabled">
+          <bool>false</bool>
+         </property>
+        </widget>
+       </item>
       </layout>
      </widget>
      <widget class="QWidget" name="tab_appearance">
@@ -461,7 +442,50 @@
      </widget>
     </widget>
    </item>
-   <item row="0" column="7" rowspan="9">
+   <item row="5" column="0">
+    <widget class="QComboBox" name="combo_spectra">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+    </widget>
+   </item>
+   <item row="9" column="8">
+    <widget class="QPushButton" name="push_exportData">
+     <property name="text">
+      <string>Export Data</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="4">
+    <widget class="QPushButton" name="pushButton">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="text">
+      <string>&amp;Close</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="3">
+    <widget class="QPushButton" name="push_options">
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="text">
+      <string>&amp;Options…</string>
+     </property>
+    </widget>
+   </item>
+   <item row="0" column="8" rowspan="9">
     <widget class="QTableWidget" name="dataTable">
      <property name="sizePolicy">
       <sizepolicy hsizetype="Fixed" vsizetype="Expanding">
@@ -517,30 +541,7 @@
      </column>
     </widget>
    </item>
-   <item row="5" column="2">
-    <widget class="QPushButton" name="push_options">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-     <property name="text">
-      <string>&amp;Options…</string>
-     </property>
-    </widget>
-   </item>
-   <item row="5" column="0">
-    <widget class="QComboBox" name="combo_spectra">
-     <property name="sizePolicy">
-      <sizepolicy hsizetype="Preferred" vsizetype="Fixed">
-       <horstretch>0</horstretch>
-       <verstretch>0</verstretch>
-      </sizepolicy>
-     </property>
-    </widget>
-   </item>
-   <item row="0" column="0" colspan="4">
+   <item row="0" column="0" colspan="5">
     <widget class="Avogadro::VTK::ChartWidget" name="plot" native="true">
      <property name="sizePolicy">
       <sizepolicy hsizetype="Preferred" vsizetype="Expanding">
@@ -572,6 +573,36 @@ Scroll wheel: Zoom to cursor</string>
      </property>
     </widget>
    </item>
+   <item row="5" column="2">
+    <widget class="QPushButton" name="push_loadSpectra">
+     <property name="enabled">
+      <bool>false</bool>
+     </property>
+     <property name="sizePolicy">
+      <sizepolicy hsizetype="Fixed" vsizetype="Fixed">
+       <horstretch>0</horstretch>
+       <verstretch>0</verstretch>
+      </sizepolicy>
+     </property>
+     <property name="text">
+      <string>&amp;Load data...</string>
+     </property>
+    </widget>
+   </item>
+   <item row="5" column="1">
+    <widget class="QComboBox" name="elementCombo">
+     <item>
+      <property name="text">
+       <string notr="true">¹H</string>
+      </property>
+     </item>
+     <item>
+      <property name="text">
+       <string notr="true">¹³C</string>
+      </property>
+     </item>
+    </widget>
+   </item>
   </layout>
  </widget>
  <customwidgets>
diff --git a/avogadro/quantumio/orca.cpp b/avogadro/quantumio/orca.cpp
index c1fe93b398..ae9a5758ef 100644
--- a/avogadro/quantumio/orca.cpp
+++ b/avogadro/quantumio/orca.cpp
@@ -60,6 +60,23 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
     return false;
   }
 
+  // this should be the final coordinate set (e.g. the optimized geometry)
+  molecule.setCoordinate3d(molecule.atomPositions3d(), 0);
+  if (m_coordSets.size() > 1) {
+    for (unsigned int i = 0; i < m_coordSets.size(); i++) {
+      Array<Vector3> positions;
+      positions.reserve(molecule.atomCount());
+      for (size_t j = 0; j < molecule.atomCount(); ++j) {
+        positions.push_back(m_coordSets[i][j] * BOHR_TO_ANGSTROM);
+      }
+      molecule.setCoordinate3d(positions, i + 1);
+    }
+  }
+
+  // guess bonds and bond orders
+  molecule.perceiveBondsSimple();
+  molecule.perceiveBondOrders();
+
   if (m_frequencies.size() > 0 &&
       m_frequencies.size() == m_vibDisplacements.size() &&
       m_frequencies.size() == m_IRintensities.size()) {
@@ -98,23 +115,6 @@ bool ORCAOutput::read(std::istream& in, Core::Molecule& molecule)
     molecule.setSpectra("NMR", nmrData);
   }
 
-  // this should be the final coordinate set (e.g. the optimized geometry)
-  molecule.setCoordinate3d(molecule.atomPositions3d(), 0);
-  if (m_coordSets.size() > 1) {
-    for (unsigned int i = 0; i < m_coordSets.size(); i++) {
-      Array<Vector3> positions;
-      positions.reserve(molecule.atomCount());
-      for (size_t j = 0; j < molecule.atomCount(); ++j) {
-        positions.push_back(m_coordSets[i][j] * BOHR_TO_ANGSTROM);
-      }
-      molecule.setCoordinate3d(positions, i + 1);
-    }
-  }
-
-  // guess bonds and bond orders
-  molecule.perceiveBondsSimple();
-  molecule.perceiveBondOrders();
-
   // check bonds from calculated bond orders
   if (m_bondOrders.size() > 0) {
     for (unsigned int i = 0; i < m_bondOrders.size(); i++) {
@@ -251,7 +251,8 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
       getline(in, key); // skip header
     }
     // starts at the next line
-  } else if (Core::contains(key, "CD SPECTRUM")) {
+  } else if (Core::contains(key, "CD SPECTRUM") &&
+             !Core::contains(key, "TRANSITION VELOCITY DIPOLE")) {
     m_currentMode = ECD;
     for (int i = 0; i < 4; ++i) {
       getline(in, key); // skip header
@@ -697,7 +698,7 @@ void ORCAOutput::processLine(std::istream& in, GaussianSet* basis)
 
           wavenumbers = Core::lexicalCast<double>(list[1]);
           // convert to eV
-          m_electronicTransitions.push_back(wavenumbers / 8065.544);
+          // m_electronicTransitions.push_back(wavenumbers / 8065.544);
           m_electronicRotations.push_back(Core::lexicalCast<double>(list[3]));
 
           getline(in, key);