Below is a simple PowerShell script you can use to create a new Web Application and thereafter a new Site Collection in that web app:
Add-PSSnapin Microsoft.SharePoint.PowerShell -ErrorAction "SilentlyContinue" | Out-Null
$name = "SharePoint 2010 Intranet"
$port = 80
$url = "http://intranet.philsdevdomain.com"
$appPoolName = "SharePointAppPool"
$appPoolAccount = Get-SPManagedAccount "philsdevdomain\spservice"
$databasename = "SharePoint_Intranet_Content_001"
New-SPWebApplication
-Name $name
-Port $port
-HostHeader $HostHeader
-URL $url
-ApplicationPool $appPoolName
-ApplicationPoolAccount $appPoolAccount
-DatabaseName $databasename
$scOwner = "philsdevdomain\phil"
$template = "STS#1"
New-SPSite -URL $url -Name $name -OwnerAlias $scOwner -Template $template
Remove-PSSnapin Microsoft.SharePoint.Powershell
Note: New-SPWebApplication will need to be on one line, and "STS#1" represents "Blank Site"