32-year-old Marc Jenkins of Rockaway Park, Queens faces up to 25 years in prison if convicted.
WABC-TV reports, Bella Edwards was found unconscious in an apartment building in the Rockaways.
Brown said that, according to the charges, Jenkins was the sole adult in the apartment with Bella and her 3-month-old sibling for about eight hours Monday.
At approximately 6 p.m., the defendant called 911 and when emergency responders arrived the little girl was unconscious and unresponsive. She was rushed to a nearby hospital, where she was pronounced dead.
The medical examiner has determined that Bella died as a result of blunt force trauma to her abdomen. Investigators are trying to determine whether she was also a victim of sexual abuse.
Jenkins was being questioned Monday at the 100th Precinct on Beach 94th Street, along with the girl's mother, Shamikaa Gonzalez.
"I cant believe it," neighbor Michelle Mevorach said. "I cant believe that because she, you wouldn't be able to see that because she was so sweet. They took very good care of her. She was never in a bad mood, Bella. Always sweet, always happy."
Police got the call around 6 p.m. Monday from a sixth-floor apartment on Beach 105th Street. They found Bella unresponsive, and Gonzalez's boyfriend was performing CPR.
Investigators believe Bella's mother was out all day on Monday. When she returned, detectives say her boyfriend told her the toddler was already sleeping. She says when she went to check on Bella later, her daughter was not breathing.
"Bella, I'm so sorry I wasn't there to protect you," Gonzalez wrote on Facebook. "This feels like a bad dream I can't wake up from. You was loved by everyone and shared so many funny memories. I'm going to miss all the times you kissed and hugged me every day."
The mother is asking friends to bring balloons and candles for Bella's vigil Wednesday night.
Investigators say Bella's injuries are consistent with that of physical abuse. One neighbor who works as a teacher and is trained to spot child abuse said she never saw anything amiss.
"I'm a mandated reporter, so I would be able to, I would think I would be able to notice these things," Laura Cabrera said. "But very well groomed, very beautiful family."
The 3-month-old sibling was taken to the hospital for evaluation.
ACS Deputy Commissioner for External Affairs Eric Ferrero released a statement:
"Our top priority is protecting the safety and well-being of all children in New York City. As soon as this family came to our attention last night, we immediately launched an investigation with the NYPD, and we secured the safety of the other child in this home."
Authorities say Jenkins served eight years in prison for attempted murder and was released in 2011.
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