Outline of how the Lexing and parsing process is going to go down.

ConditionParser.cs

void Main()
{
    //The user input expression
    var expression = "\"java\" and \"SQL\" and \"C#\" or \"VB.NET\""; 
    
    //The collection of tokens that we will use to evaluate the logic in the expression
    var tokens = Tokenize(expression);
    //tokens.Dump();
    
    //Our evaluated representation of the tokens; We can use this to 
    //convert the expression to whatever language we wish
    var ConditionNode = Eval(tokens);
    
    //Transforms our Nodes into our desired programming language
    var endResult = CreateQueryString(ConditionNode );
    
}

// Define other methods and classes here
public static List<string> Tokenize(string expression)
{
    var tempExpression = System.Security.SecurityElement.Escape(expression);
    string doubleQuote = "&quot;";
    var regEx = string.Format("(not\\s+)?{0}(.+?){0}(and|or)?",doubleQuote);

    Regex RE = new Regex(regEx);
    var result = (RE.Split(tempExpression)).Select (r => r.Trim());
    return result.Where (re => !String.IsNullOrWhiteSpace(re)).ToList();
}

public enum LogicalOperator
{
    None = 0,
    And = 1,
    Or = 2,
}

public static LogicalOperator ParseOperator(string expression)
{   
    var retval = LogicalOperator.None;
    switch (expression.Trim().ToLower())
    {
        case "and":
            retval = LogicalOperator.And;
            break;
        case "or":
            retval = LogicalOperator.Or;
            break;
        default:
            retval = LogicalOperator.None;
            break;
    }
    return retval;
}

public static Condition Eval(List<string> tokens)
{
    var retval = new Condition();
    var tempPtr = retval;
    for(var i=0;i<tokens.Count();i++)
    {
        if(tokens[i].ToLower()=="not")
        {
            tempPtr.HasNot = true;
        }
        else if(tokens[i].ToLower()=="and"||tokens[i].ToLower()=="or")
        {
            tempPtr.LogicalOperator = tokens[i].ToLower()=="and"?LogicalOperator.And:LogicalOperator.Or;
            tempPtr.Right = new Condition();
            tempPtr = tempPtr.MoveRight();
        }
        else
        {
            tempPtr.expression = tokens[i];
        }
    }
    return retval;
}

public class Node
{
}

public class Condition:Node
{
    public int Order {get;set;}
    public string expression {get;set;}
    public LogicalOperator LogicalOperator {get;set;}
    public bool HasNot{get;set;}
    public Condition Right {get;set;}
}

public static class ConditionExt
{
    public static Condition MoveRight(this Condition node)
    {
        return node.Right;
    }
}

public static string CreateQueryString(Condition node)
{
    StringBuilder sb = new StringBuilder();
    while (node!=null)
    {
        if(node.HasNot)
        {
            sb.Append("Not ");
        }
        sb.Append(node.expression+" ");
        if(node.LogicalOperator!=LogicalOperator.None)
        {
            sb.Append(Enum.GetName(typeof(LogicalOperator), node.LogicalOperator) +" ");
        }
        node = node.Right;
    }
    return sb.ToString();
}

LexFlow.cs

void Main()
{
    //The user input expression
    var expression = "\"java\" and \"SQL\" and \"C#\" or \"VB.NET\""; 
    
    //The collection of tokens that we will use to evaluate the logic in the expression
    var tokens = Tokenize(expression);
    //tokens.Dump();
    
    //Our evaluated representation of the tokens; We can use this to 
    //convert the expression to whatever language we wish
    var ConditionNode = Eval(tokens);
    
    //Transforms our Nodes into our desired programming language
    var endResult = CreateQueryString(ConditionNode );
    
}

OpManagement.cs

public enum LogicalOperator
{
    None = 0,
    And = 1,
    Or = 2,
}

public static LogicalOperator ParseOperator(string expression)
{   
    var retval = LogicalOperator.None;
    switch (expression.Trim().ToLower())
    {
        case "and":
            retval = LogicalOperator.And;
            break;
        case "or":
            retval = LogicalOperator.Or;
            break;
        default:
            retval = LogicalOperator.None;
            break;
    }
    return retval;
}

TheConditionEvaluator.cs

public static Condition Eval(List<string> tokens)
{
    var retval = new Condition();
    var tempPtr = retval;
    for(var i=0;i<tokens.Count();i++)
    {
        if(tokens[i].ToLower()=="not")
        {
            tempPtr.HasNot = true;
        }
        else if(tokens[i].ToLower()=="and"||tokens[i].ToLower()=="or")
        {
            tempPtr.LogicalOperator = tokens[i].ToLower()=="and"?LogicalOperator.And:LogicalOperator.Or;
            tempPtr.Right = new Condition();
            tempPtr = tempPtr.MoveRight();
        }
        else
        {
            tempPtr.expression = tokens[i];
        }
    }
    return retval;
}

TokenizingTime.cs

// Define other methods and classes here
public static List<string> Tokenize(string expression)
{
    var tempExpression = System.Security.SecurityElement.Escape(expression);
    string doubleQuote = "&quot;";
    var regEx = string.Format("(not\\s+)?{0}(.+?){0}(and|or)?",doubleQuote);

    Regex RE = new Regex(regEx);
    var result = (RE.Split(tempExpression)).Select (r => r.Trim());
    return result.Where (re => !String.IsNullOrWhiteSpace(re)).ToList();
}

WhereMyNodeAt.cs

public class Node
{
}

public class Condition:Node
{
    public int Order {get;set;}
    public string expression {get;set;}
    public LogicalOperator LogicalOperator {get;set;}
    public bool HasNot{get;set;}
    public Condition Right {get;set;}
}

public static class ConditionExt
{
    public static Condition MoveRight(this Condition node)
    {
        return node.Right;
    }
}

public static string CreateQueryString(Condition node)
{
    StringBuilder sb = new StringBuilder();
    while (node!=null)
    {
        if(node.HasNot)
        {
            sb.Append("Not ");
        }
        sb.Append(node.expression+" ");
        if(node.LogicalOperator!=LogicalOperator.None)
        {
            sb.Append(Enum.GetName(typeof(LogicalOperator), node.LogicalOperator) +" ");
        }
        node = node.Right;
    }
    return sb.ToString();
}