Running late after a brief visit to his laboratory, a hurried Andy Hamilton walked into his first-floor office in Warner House at 9:30 one morning last spring. Apologizing to a visitor waiting for him, he grabbed a tie off his desk, walked over to a mirror in the back of his office and put it on.

Then he sighed. “Chemists don’t wear neckties,” Hamilton explained. “Provosts wear neckties.”

It can be said that Hamilton, who is now enjoying the first week of what he calls a “gap year” before he becomes vice-chancellor of the University of Oxford next fall, is still a scientist first, an administrator second. And professors on Science Hill say it was that passion that allowed the smartly tailored Briton to leave such a mark on the sciences at Yale.

Indeed, it is fitting that Hamilton, who departed Warner House last Wednesday, is not taking the next year off — but rather returning to his laboratory to focus on his research.

“He’s been a terrific leader for science at Yale,” University President Richard Levin said.

Just over a decade ago, Hamilton wore a Salovey-esque mustache and taught chemistry at the University of Pittsburgh. Next year, he will take the helm of the oldest university in the English-speaking world.

In a conversation during his final days in office, Hamilton — Yale’s chief academic officer and its top official after the president — reflected on that speedy ascent since he joined the Yale faculty as a chemistry professor in 1997 and, two years later, took the helm of his department.

“I’m a scientist. I still sometimes pinch myself: How did I walk into this administrative world?” he said. “Five years ago, I was doing the normal duty of many professors in their departments of being departmental chair, expecting at the end of my term to go back to the lab.”

But in 2003, then-Provost Susan Hockfield persuaded Hamilton to join the Provost’s Office as deputy provost for science and technology. When Hockfield left for the presidency of the Massachusetts Institute of Technology a year later, Levin tapped him for the provostship.

Hamilton’s scientist roots, however, did not fade. “He occasionally entertained the Faculty of Arts and Sciences Steering Committee with soliloquies on various chemistry topics such as the poorly understood nature of lignin fibers in wood,” said Steve Girvin, the current deputy provost for science and technology.

But he also came into his own as an administrator, professors said. As with Hockfield and her two predecessors, Hamilton seemed a sure bet to assume a university presidency — perhaps that of the University of Cambridge, where he received his doctorate and where another former Yale provost, Alison Richard, is now at the helm.

But Oxford came calling in the springtime. “Initially, I didn’t leap at the opportunity in the main because I was happy and contented in my role here,” Hamilton said. “But it was after a couple of trips over, many conversations with people both there and here that I came to the conclusion that it was the right place for me at the right time in my career.”

Hamilton, for one thing, continued his predecessors’ efforts to chip away at Yale’s longstanding reputation as a top-flight humanities school but not a top-flight school for the sciences.

Hockfield praised him for helping to continue investing aggressively in the sciences and challenging that perception. “Andy Hamilton just seamlessly picked up the baton and has accomplished a huge amount,” she said in a telephone interview last week. “It’s exciting to see.”

His achievements as provost included overseeing Yale’s continuing $1 billion investment in the sciences, medicine and engineering programs, and the rebirth of the School of Engineering as its own professional school.

Plus, there was the West Campus.

“Certainly the most consequential step taken during Hamilton’s time as provost was the purchase of the Bayer site in West Haven,” Sterling Professor of Chemistry Peter Moore said.

The real test of the decision, he added, will be whether West Campus ends up enhancing science research ongoing at the University or weakening Yale by diverting resources and attention away from the main campus.

“Both Hamilton’s legacy and Levin’s will be determined in no small measure by how the West Campus venture plays out,” Moore said.

Other Yale administrators enjoyed poking fun at their chemist colleague for his affection for the former site of Bayer HealthCare, which the University acquired in 2007 in what Levin called a once-in-a-century opportunity. They joke that Hamilton — an organic chemist — salivated when he first toured through the campus’ hundreds of thousands of feet of state-of-the-art laboratories.

“He loses it,” quipped Roland Betts ’68, the senior fellow of the Yale Corporation, the University’s highest governing body. “He gives tours over there and he can’t even talk.”

But science professors here say the work he has done in improving the sciences is no joke.

Even before he ascended up the ranks to provost, as chemistry chair, Hamilton laid the groundwork for the completion of the Class of 1954 Chemistry Building — a project that had stalled in its planning stages for the better part of a decade before its construction finally began, said Gary Brudwig, current chair of the Chemistry Department.

The promise of the new building—which would significantly increase the amount of research space available to the Chemistry Department—was pitched to attract the provost to the University 11 years ago, but it was a promise that was not fulfilled until much later during his time at Yale. Construction on the building began just over four years ago — nearly seven years after Hamilton took up his appointment as chemistry chair — and was dedicated in October 2005.

But it was Hamilton, Brudwig said, who did the legwork to get the approvals on the building’s construction and gave the final “go.”

“It was one of the things that occupied his time,” he said. “He deserves a lot of credit for it.”

Even alongside all his administrative responsibilities, Hamilton maintained a lab that never slowed down a step, Girvin said.

“Andy felt strongly … that it was important for administrators to remember the realities of how hard it is to do frontier research,” he said. “How he managed to do this given the demands of his job is totally beyond me.”

Hamilton’s less public role is at the helm of a lab that probes the science of molecular recognition and self-assembling molecules, and applies contemporary knowledge about molecular interaction to the development of drugs that halt human cancers.

In addition to his full plate of research responsibilities — churning out grant applications and research journal articles — Hamilton still managed to meet with his laboratory research group weekly, Brudwig said.

For Hamilton, there were other highlights beyond science, too. He helped lead several successful efforts to recruit A-list professors in a range of departments. He shepherded through the reform of Yale’s tenure system. When the Faculty of Arts and Sciences unanimously approved the new tenure system in 2007, Hamilton was the one who was charged with calling for the official vote. When he asked the faculty for nay votes and heard silence — literally — it was a special moment, he said.

Hamilton may face more dissent at Oxford, which is known for the relative assertiveness of its faculty. But Hamilton’s skills as a manager could help him succeed in what some professors here privately said is among the most difficult jobs in higher education.

“He has the capacity to make everyone he meets think he sympathizes with them,” Moore said. “This is a huge asset. Good politicians are able to do this. You cannot long succeed in a post like the one Hamilton has held if you do not have it.”

Hamilton will remain in New Haven until summer, but on Sept. 26, he received a glamorous send-off in Commons. Mascots from his previous schools roamed the room, photographs from his past revealed his stunning mustache and the Gilbert and Sullivan Society — with the help of a few special guests, like Deputy Provost Charles Long — sufficiently embarrassed him with two personalized tunes written for the occasion, including “Behold the Oxford Lord Vice Chancellor.”

When Hamilton came to Yale from Pitt, he brought a laboratory of 14 graduate students and postdocs with him. And as he heads to Oxford, so will his laboratory.

Even as the leader of one of the foremost universities in the world, Hamilton said he will still find time to take off his necktie and return to his lab.

“It will be a challenge, but I have actually found that continuing my research in this role actually helps me to do my job as an administrator,” he said. “It’s the reason I began this career 27 years ago as an assistant professor. It allows me to maintain my sanity.”