-S {.}.sam, not S- i.sam

As for the above for loop, it would be:

for i in /mnt/d/Chipseq/Hchipseq/*.fastq
  do
  bowtie2 -p 16 --fast-local --no-mixed -t -x hg19 -U "${i}" -S "${i%.fastq}".sam
  done

Pro tip, save disk spave by piping the output into samtools view or sort, e.g.

for i in /mnt/d/Chipseq/Hchipseq/*.fastq
  do
  bowtie2 -p 16 --fast-local --no-mixed -t -x hg19 -U "${i}" | samtools view -o "${i%.fastq}".bam
  done

The "${i}" in each iteration is one of the fastq files, and the "${i%.fastq}" strips the fastq suffix so you can append a new one such as .sam/.bam. Be sure to spend quality time on Unix basics. Even if you use stuff like workflow managers they are at some point all based on plain Unix, and proper knowledge of that is a good investment of time.