Use Xpath to simplify your life! As you haven't posted the full xml file you are after, I assume that it should look like :

<root>

<predicted_properties>
<property>
    <kind>water_solubility</kind>
    <value>0.00169 mg/mL at 25 C</value>
    <source/>
</property>
</predicted_properties>

<predicted_properties>
<property>
    <kind>formal_charge</kind>
    <value>-1</value>
    <source>ChemAxon</source>
</property>
</predicted_properties>

</root>
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The code looks for the 'kind' node and then for its sibling node called 'value'

use XML::Twig::XPath;

my $twig= XML::Twig::XPath->new();
$twig->parsefile('myfile.xml');

print $twig->findvalue
('/root/predicted_properties/property/kind[text()="formal_charge"]/
following-sibling::value');
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prints -1

One suggestion to simplify your xml structure would be to add it as an attribute to kind. ie :

<kind name='formal_charge'>-1</kind>
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